University of Central Florida STARS
UCF Patents Technology Transfer
10-7-2014
Microarrays of Binary Nucleic Acid Probes for Detecting Nucleic Acid Analytes (US)
Dmitry Kolpashchikov
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Recommended Citation Kolpashchikov, Dmitry, "Microarrays of Binary Nucleic Acid Probes for Detecting Nucleic Acid Analytes (US)" (2014). UCF Patents. 758. https://stars.library.ucf.edu/patents/758 I lllll llllllll Ill lllll lllll lllll lllll lllll 111111111111111111111111111111111 US008853134B2 c12) United States Patent (IO) Patent No.: US 8,853,134 B2 Kolpashchikov (45) Date of Patent: *Oct. 7, 2014
(54) MICROARRAYS OF BINARY NUCLEIC ACID 2219100722 (2013.01); C12Q 116837 (2013.01); PROBES FOR DETECTING NUCLEIC ACID BOJJ 1910046 (2013.01); C40B 50118 ANALYTES (2013.01); BOJJ 2219100612 (2013.01); BOJJ 2219100608 (2013.01); BOJJ 2219100529 (75) Inventor: Dmitry Kolpashchikov, Winter Park, FL (2013.01) (US) USPC ...... 506/13; 506/16 (73) Assignee: The Trustees of Columbia University (58) Field of Classification Search in the City of New York, New York, NY USPC ...... 506/13 (US) See application file for complete search history. (56) References Cited ( *) Notice: Subject to any disclaimer, the term ofthis patent is extended or adjusted under 35 U.S. PATENT DOCUMENTS U.S.C. 154(b) by 0 days. 6,413,722 Bl 7/2002 Arnoldetal. This patent is subject to a terminal dis 200210172960 Al 1112002 Bao et al. claimer. (Continued) (21) Appl. No.: 13/146,626 FOREIGN PATENT DOCUMENTS (22) PCT Filed: Jan.28,2010 EP 0853129 * 7 /1998 Cl2Q 1168 (86) PCT No.: PCT/US2010/022428 WO 92/20823 Al 1111992 (Continued) § 371 (c)(l), OTHER PUBLICATIONS (2), ( 4) Date: Aug. 26, 2011 Kolpashchikov, Binary Probes for Selective Nucleic Acid Recogni tion, 2007, Book of Abstracts:2007.* (87) PCT Pub. No.: W02010/088404 (Continued) PCT Pub. Date: Aug. 5, 2010 Primary Examiner - Larry Diggs (65) Prior Publication Data Assistant Examiner - Karla Dines (74) Attorney, Agent, or Firm - Timothy H. Van Dyke; US 2012/0040867 Al Feb. 16, 2012 Beusse, Wolter, Sanks & Maire, P.A.
Related U.S. Application Data (57) ABSTRACT Some embodiments ofthe invention are directed to a microar (60) Provisional application No. 61/147,993, filed on Jan. ray of binary nucleic acid probes for the detection of one or a 28, 2009. plurality of nucleic acid analytes in a complex sample in a single high throughput assay with extraordinary specificity (51) Int. Cl. under physiologic conditions. Any binary nucleic acid probes C40B 40106 (2006.01) that generate a detectable signal when bound to analyte are C40B 80100 (2006.01) suitable for use in the microarrays, including binary deoxyri bozyme or ribozyme probes; nonenzymatic binary probes for C12Q 1168 (2006.01) fluorescent detection, nonenzymatic binary dye-binding BOJJ 19100 (2006.01) probes, and binary split enzyme peroxidase probes for visual C40B 50118 (2006.01) detection of nucleic acids. The invention is also directed to (52) U.S. Cl. new non nonenzymatic binary probes that bind to reporter CPC ...... C40B 80100 (2013.01); BOJJ 2219100659 oligonucleotides. (2013.01 ); BOJJ 221910061 (2013.01 ); BOJJ 7 Claims, 11 Drawing Sheets
NONENZYMATIC BINARY NUCLEIC ACID PROBES BINDING TO MOLECULAR BEACONS
SEQ ID 14 US 8,853,134 B2 Page 2
(56) References Cited pp. 10625-10628, vol. 128, Publisher: American Chemical Society, Published in: US. U.S. PATENT DOCUMENTS Kolpashchikov, Dmitry M., "A Binary Deoxyribozyme for Nucleic Acid Analysis", "ChernBioChern", 2007, pp. 2039-2042, vol. 8, 2007/0231810 Al 10/2007 Todd et al. Publisher: Wiley-VCR Verlag GmbH & Co., Published in: Germany. 2009/0176318 Al 7/2009 Kolpashchikov Kolpashchikov, Dmitry M., "Split DNA Enzyme for Visual Single Nueleotide Polymorphism Typing", "Journal of American Chemical FOREIGN PATENT DOCUMENTS Society", Mar. 12, 2008, pp. 2934-2935, vol. 130, No. 10. Marras et al, "Real-time assays with molecular beacons and other WO 2007 /115242 A2 10/2007 fluorescent nucleic acid hybridization probes", "Clinica Chimica WO 2008/054834 A2 5/2008 Acta", Aug. 18, 2005, p. 48-60, vol. 363, Publisher: Elsevier B.V. WO 2010/059944 Al 5/2010 Mokany et al., "MNAzymes, a Versatile New Class of Nucleic Acid Enzymes That Can Function as Biosensors and Molecular Switches", OTHER PUBLICATIONS "J. Am. Chem. Soc.", 2010, pp. 1051-1059, vol. 132, No. 3, Pub lisher: American Chemical Society. Xiao et al., Catalytic Beacons for the Detection of DNA and Isa, "International Preliminary Report on Patentability for Corre TelomeraseActivity, J.Am. Chem. Soc., 2004, 126, pp. 7430-7431.* sponding International Application No. PCT /US2010/022428", Aug. Kolpashchikov, A Binary Deoxybibozyme for Nucleic Acid Analy 2, 2011, pp. 1-8, Published in: Switzerland. sis, Chembiochem, Nov. 23, 2007, 8(17), pp. 2039-2042. * Isa, "International Search Report and Written Opinion for Corre Babendure et al., "Aptanners Switch on Fluorescence of sponding International Application No. PCT/USl0/22428", Mar. 19, Triphenylmethane Dyes", "J. Am. Chem. Soc.", Nov. 8, 2003, pp. 2010, pp. 1-12, Published in: US. 14716-14717, vol. 125, Publisher: American Chemical Society, Pub Sando et al., "Light-Up HoechstDNAAptamerPair: Generation of an lished in: US. Aptamer-Selective Fluorophore from a Conventional DNA-Staining Bonnet et al, "Thermodynamic basis of the enhanced specificity of Dye", "ChemBioChem", 2007, pp. 1795-1803, vol. 8, Publisher: structured DNA probes", "Proc. Natl. Acad. Sci.", May 1999, pp. Wiley-VCR Verlag GmbH & Co., Published in: Germany. 6171-6174, vol. 96, Published in: US. Tyagi et al., "Molecular Beacons: Probes that Fluoresce upon Kolpashchikov, Dmitry M., "Binary Malachite Green Aptamer for Hybridization", "Nature Biotechnology", Mar. 1996, pp. 303-308, Fluorescent Detection of Nucleic Acids", Aug. 19, 2005, pp. 12442- vol. 14, Publisher: Nature Publishing Group. 12443, vol. 127, Publisher: American Chemical Society, Published Kolpashchikov, D. et al., "Boolean Control of Aptamer Binding in: US. States", J. Am. Chem. Soc., 2005, vol. 127, pp. 11348-11351. Kolpashchikov, Dmitry M., "A Binary DNA Probe for Highly Spe cific Nucleic Acid Recognition", "J. Am. Chem. Soc.", Jul. 21, 2006, * cited by examiner U.S. Patent Oct. 7, 2014 Sheet 1of11 US 8,853,134 B2
>< .· . w .$:: : .·.· _J ·:·····: 0... (~ l.~-' '-"-· ~ ~~~ ,., -~ .. ~ l l .$ c l 0 l _g; "'::..~ l l 0 i)'',• l l l ~.,., l w l m l l Q l co ·;;;: l J l <)) c l 0 l Q'> l ,\:..l__ l l a:: >:I l l l 0... 2 l w... l ,l 0-- ~ ~ >- zN w ~ <( z co I I- s a::~ a:: <( 0 ...... a:: 0 C) -- LL ~ U.S. Patent Oct. 7, 2014 Sheet 2of11 US 8,853,134 B2
0- ~ ~ >- Nz w ~ <( z co LL 0 I-z w ~ C) <(a:: LL w z 0 I I- s m a::~ a:: <( w 0 co a:: 0 0 a:: ~ 0... N C) <( LL ~ 00 • ~ FIG. 3 ~ MICROARRAY WITH ONE STRAND OF BINARY ~ PEROXIDASE-LIKE PROBE ~ =~
0 A p., tmgrnent ot peroxidase-like .r-,.,....._., (') Array of binary B C I \/ .... Anniyk"·,··:• !, deoxydtm;r.yrne probes ;/ DNf\ enzyme "'.....:i t)A '"-.,, 'l '· ;;: 1 o ';"------,,~ 1 r·~emm N _" y).....,..J/... ~/ ... t ...... ~...) ...... ) ...)~ ... ) ..."'. \_cl. .~::::-:·::::::--//~ 0.... r·~ . _:::;, .i;... 1+ Second fragment of deoxydbozyme catalyUc corn 1J1 ('D= ('D..... C' Anatyte with a mismatch (.H 0..... Achve pemx!dase-liktJ + -~-'-- ··...... J;) Hern1~ .... <%,:' '.~)('%, DNAr;nzyme (I ()'\,'- ___ ,,, 4,,...) "'""""'"""' ,, in ccmplex vvith hemin v ,l,J,,;,,,,,,,,;,,~,,,,,,;, 11{' /' ......
D <~;\:\~:v/ = .,• r, .,~ •" • ;: • ;.• '. • •: •:• n ~:;·f;L--~~-~;:!; f3 E DAB-:::- c0brnd products d .,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,._ rJl. ·· \/isua~~Y 00 ...... Oo wtit "' w""'"' ~ =N U.S. Patent Oct. 7, 2014 Sheet 4of11 US 8,853,134 B2
w co 0 a:: 0... ~ <( z co C) -z 0 z co coI ~ LL 0 0 z <( a:: I- CJ) w z 0 I I- s + a::~ a:: <( ~ 0 a:: C) 0 LL - ~ ~ 00 • ~ FIG. 5 ~ ~ ~
BINARY DEOXYRIBOZYME PROBE STRAND STRUCTURE =~
00 A11..1;i,f " n H ...... :- ~t >-~· ·~-- :/ w co 0a:: 0... w ~ N>- 0 co a:: >- >< 0 w 0 ::;~ ~~· ~". $; ~:;:~ ~ '':.~~· ~ .:-.:. <( ·$»'""" ~ ·~? z w :~~~ w ~ ~~ co :a ~:;:~ :.~~ ·~ A) P0r(YKldnse.,t)ke DNJ\ rm2yme ~ 5'A3-G-G-T-A~G-G-G,,;c.c: c;:c. T ·. T .c;..c. "' SElJ IIJ 5 =~ l I l 8} Birwfy DNA pmoxi dase • S.EQ ID 8 0 (') ~ ~;EQ ID G .> ~·:: ·:' ::.. ·:·. ::::::: : ·; .. , ..... 6,, o"'P ,(). G--G-G-T~A-G-G-G > "'-...J ,~6 p c/ 9 N Analyte blndirlg amm J. ! 0 \.:;--·~ (J, 4. Q;o;P,{T' .... fi • • C·-C-C,J\-C-G--TG .6 .i;... \,,(1-G-T-C·C·T·G-T-G·C-C-S' ~;Er.J ID: 7 ~SEQ ID 9· DNA. aneiyte and hemin {4.l"KL211M~) ! 1J1 ('D= ('D..... C) -...J n'f~~~:~G. 0 -G·-~;~~· G ...... -0-~~~~-: (; .... SEQ ID 9 }~ , : q; "'"2421'"f;;-Y-G . c-c,-c,;~,c,.(::f,T-G G-T-'C-C-T-G,.T-G-C-C,.5' SE~J IL} 10 ti>·· ,,xir ;i I l ! I ! l ! I i i I i i i I I I I 5-T43-G-C-T-T-C-G-C>C-C-A-G-G-G-T-G-C-A-C.i-C"A-G-G;.A-C-A.-C-G-G-T-T-T-T / ..... ,, ...... ~---. ---.., SE~J ID 11 // "\ d ·l-H:,O:: \ rJl I -~' 00 Colorless substrate Colored pnxluct Oo wtit "' w""'"' ~ =N ~ 00 • ~ FIG. 8 ~ ~ ~ NON ENZYMATIC BINARY NUCLEIC ACID PROBES BINDING TO =~ MOLECULAR BEACONS 0 ...... (') 90P1NW 11>~ ·1 < ~.....:i A SEQ ID ~ _( ;tA'"'G'" /,:. {~~~·<:~ Ji~. SEQ 1J1 f.f--.<>;:;~t·A:{}..Z:;;T:-c: ;.~ .·r-· ..r4'vf%·~t::>r·:rt~ ('D= ('D A1fl1 t#r~#if.~~ 6:.:-?:::%~ S FAM D~br;:yl ..... QO 0 I ,,_ ....,. ,-'%_,,. ,.. ,... ,, .. ,,,,...... +"'·""' _,.,,,,, .,,.,,,.,., A:~~ {~fJ.A: 1N?.~¥y1~: 1;:; .:~: ··l~·:f-:f~"<>A:<~>.fv<>fo~>::::Fr~C?(1~1.?f·T~~)·>(>{Yf~{) s EQ I I) ·-< r.14~:i'J:~A:>s·1; .-i;-C ·-i!:>Y ..(;., -f-.C>-T>-~:: 7.~-0-(>0> jk:.f>G;{>~~--t>r.(J,.rr-c>T ·-ff ~3E·Q ID 12 A SE1'.J ID 1 ..3 ~ a -g~,.<>A--T4~:·~(~·;(~8~:r:-... c:: l--T~t~> k_,{~:r ..~ ·{~ d 'ii· '* ~ ~ ~ 11:'" '* « * {': +: 'k ),I< :ff.+ fl\. ).:;;rfY·(~-<>-r~;><7.-T"#{"f~(:'-C-/~~~(~-P-:'·A-T;,T· FIG. 9 =~ BINARY DYE-BINDING PROBE MGA 0 a biMGA probe b c .....(') A ,, .. ,,.,,,,t;r! C G 5' v·: "'-....J G •(;j N G• SEQ ID I-JO., 1.:9 ?c~·c1 c G•Ci Stem-2 0.... G ,.r"! G• .i;... u c U•A! •G•c! •A C•Gir·· •u • A~ Stem-2 C• GGU •.,,,.L,,,,GJGC• i A ~~-~?#' A G ~.r-A ,~,, A U~~- G .....,r·A ,...,y•~-> ~· 1J1 . ~Wf.iMW°"' G-.cAfa~ c zj%f[[!.1%.W r·•GA ('D= ~.mf.Afiw' 4" --~ •GAA '--' A ('D..... 1..,,•t;JA,,.... ,..., c •GU rc~•--c1u ...... A C• G "°0 :c~c~•u· I c. Gl Stem-1 ..... 'e ; . u •A L.U. ..! .. .Al .... ' .... •G' u .... ! U• A! u u u ! A • ui Stem-1 uu i's'.c;"{;,,p;·c:,,c:,,c"Z: s'·vQ r:: c· A..,.-....svv, r r. r: A c· U• C U e'wl U 1V ' i (J • c! [;,::!Jj~~:1L9:!J::QJ SEQ I[l NO. 17 .,_ •'llf ii •••••••• '*' ••• II' :~!II cl nucleic add binding arms c g t g g g t g a g a g. a g 5' SEQ ID !-JO. 18 EE(l ID 16 d rJl. 00 Oo wtit "' w""'"' ~ =N U.S. Patent Oct. 7, 2014 Sheet 10 of 11 US 8,853,134 B2 Cf) w ca 0 o::'. 0.... o::'. w ~ ~ 0.... <( ~ + <( z ca . CJ LL ~ 00 • ~ ~ ~ FIG. 11 ~ =~ BINARY REPORTER OLIGONUCLEOTIDE-BINDING PROBE 0 ....(') "'--.J N Analyk'·,.4 .... 0 Array of binary binrlmg~O arm r-;;_ 9(? ~df(fjt~@R WI ~"'.'°~""."""".""~""."".,...~~~ .,,~J~~~i .... deoxyribozyme probes .i;... ;/ I G/ ';-,-;;-WJJ. \ - ,,,,,,,,,,,,,,,,,,,_ strand (L + ~t~~~~J~,,,,: Reporter.,,,, w,,,,,,,,,,,,,,,i . A!i:>otide: \RO) 1 ohgonu._, ~ 1J1 ('D= ('D...... 0...... a) Organic F!uorophore ffl~~ b) Quantum dot c) Gold nanopartide d) Biotin d rJl 00 Oo tit w "' w"'""" ~ =N US 8,853,134 B2 1 2 MICROARRAYS OF BINARY NUCLEIC ACID FIG. 3 Scheme of the array of binary oligonucleotide per PROBES FOR DETECTING NUCLEIC ACID oxidase probes for visual (colorimetric) detection of nucleic ANALYTES acids. A: A chip (solid support) contains an array of oligo nucleotides. B: As in FIG. 2, the first strand of the probe STATEMENT OF GOVERNMENTAL INTEREST 5 having a fragment alpha includes the catalytic core of the peroxidase-like DNA enzyme(blue) and analyte-binding arm This research was made with US government NIH, (green line) is attached to the solid support via Linker 1 NHGRI R21_HG004060. (dashed line). C: In this example the second strand that has the second fragment of the deoxyribozyme catalytic core (beta, BACKGROUND OF THE INVENTION 10 orange) provided separately, hybridizes to the analyte in solu tion. C': In this example the second strand of the deoxyri 1. Field of the Invention bozyme probe hybridizes with analyte containing a single base mismatch. D: Catalytically active peroxidase-like DNA The present invention relates to binary nucleic acid probes enzyme is formed only in C where the analyte-binding arms arranged on a microarray for nucleic acid analysis. 15 are fully complementary to the analyte. The reformed peroxi 2. Description of the Related Art dase catalytic core forms a G-quadruplex that binds hemin The growing importance of sensitive and selective deter from the solution and decomposes hydrogen peroxide; the mination of nucleic acids is associated with detection of decomposition products convert a colorless substrate such as viruses, microorganisms, and genetic traits that are not only DAB (3,3'-diaminobenzidine) to a water insoluble colored of clinical significance, but also of environmental, defense, 20 product that can be detected. E: The water-insoluble product veterinary and agricultural importance. Simple and sensitive forms brown spots on the array. sequence-specific methods of nucleic acid analysis are FIG. 4. Scheme of SNP analysis by an array of binary needed, for example, for the rapid diagnosis of infection and nonenzymatic DNA probes that have molecular beacon-bind genetic diseases, genome study, mRNA monitoring in living ing arms. A: The first strand ofthe nonenzymatic binary pro be cells, for environmental and forensic applications. Binary 25 is immobilized on a solid support via a linker attached to the nucleic acid probes that have extraordinary selectivity and analyte-binding arm. B: The second strand is hybridized specificity, can be used at ambient temperature, are low cost, separately with the nucleic acid analyte in solution. C: The and adaptable for fluorescent or visual detection have been strand/analyte hybrid is added to the microarray and the ana described. However there is still a need for microarrays of the lyte-binding arm on the first strand hybridizes with the ana- binary probes that enable high throughput analysis of a com 30 lyte, causing the two halves of the probe to hybridize that in plex mixture of nucleic acids and for new binary probes for turn causes the molecular beacon-binding arms on each detecting them. strand of the binary probe to hybridize with a molecular beacon that was included in the solution to form fluorescent BRIEF DESCRIPTION OF THE DRAWINGS complex. D: The fluorescent complex is not formed if the 35 analyte is not fully complementary to the analyte-binding arm The present invention is illustrated by way of example, and ofBDP strand. not by way oflimitation, in the figures of the accompanying FIG. 5 is a schematic of an embodiment of one of the two drawings and in which like reference numerals refer to similar oligonucleotide strands of a binary deoxyribozyme probe. elements. FIG. 6 shows the structure of the two strands of the biE6- FIG.1.A: Variant of deoxyribozyme array in which the two 40 1Oh binary enzymatic probe which in this embodiment has a oligonucleotide strands of the binary probe are joined via structure stabilization arm attached to each analyte-binding Linker 2 (cyan) to make a single stranded binary probe com arm that form a stem loop structure in the absence of analyte. plex that is immobilized on a solid support at a particular site In the left panel the two strands are separate. The sequence of on the microarray via another linker. This binary probe com a fluorescent substrate for the enzyme is shown. In the pres plex contains two fragments of deoxyribozyme catalytic core 45 ence of analyte, the stem loops open, the analyte-binding (black) connected via Linker 2. The single DNA strand mak arms bind to the analyte, the probe-binding arms hybridize ing up the binary probe complex is in tum attached to the solid reconstituting the catalytic core of the deoxyribozyme, and support via Linker 1 (orange). B: Active deoxyribozyme is the substrate-binding arms bind the fluorescent substrate formed in the presence of DNA analyte that hybridizes to the (Center Panel). In the right panel, the activated enzyme analyte-binding arms on the binary probe complex. C: The 50 hydrolyzes the substrate generating a detectable fluorescent deoxyribozyme cleaves a fluorogenic substrate generating a substrate. fluorescent signal. FIG. 7 Design of an embodiment of a binary DNA peroxi FIG. 2. Array of binary deoxyribozymes for fluorescent dase for SNP analysis. A: Parent peroxidase-like DNA detection of nucleic acids in which A: each feature has one enzyme. B: Binary DNA peroxidase probe. C: The probe strand ("the first strand") of a binary deoxyribozyme probe 55 forms active peroxidase upon hybridizing to the abutting immobilized on a solid support via a linker (red dashed line). positions of the analyte. The enzyme catalyzes oxidation of a The first strand includes a fragment of the deoxyribozyme colorless substrate to colored products. The triethylenglycol catalytic core (black). B: The second strand of the binary linkers are shown as dashed lines in panel C. The SNP site in deoxyribozyme probe that contains the other half of the cata the analyte sequence is underlined. lytic core (blue) is supplied separately. In this example the 60 FIG. 8 Primary and secondary structure of an embodiment second strand is mixed with the target analyte that binds to the of a binary DNA molecular beacon-binding probe (BDPs) A: analyte-binding arm (green) forming a strand/analyte hybrid. Structure of the BDP10/8sl probe in the absence (top) or The hybrid is then added to the microarray. The immobilized presence (bottom) of A20 DNA analyte. B: Structure of first strand binds the analyte causing the two halves of the strands A and B of BDP8/8 and BDPl0/8. C: Structure of binary probe to hybridize reforming the active catalytic core. 65 strands A and B ofBDP10/8sl F .tu!. The triethylene glycole C: The active DNAzyme cleaves a fluorogenic substrate and linkers are depicted by the dashed lines on the panels A increases the fluorescence of the feature. (bottom), B and C. US 8,853,134 B2 3 4 FIG. 9 (a) Structures of an embodiment of a MGA (mala "ribozyme" includes endoribonucleases and endodeoxyribo chite green aptamer) in complex with MG (malachite green nucleases, although deoxyribozymes/ribozymes with endori dye). (b) The biMGA RNA probe free in solution. (c) biMGA bonuclease activity are particularly preferred. Other terms probe bound to complementary DNA analyte. Ribonucle used interchangeably with deoxyribozyme/ribozyme herein otides are represented in uppercase whereas deoxyribo are "enzymatic DNA/RNA molecule", "DNAzyme/ nucleotides are in lowercase. RNAzyme", or "catalytic DNA/RNA molecule", which FIG. 10. Is a schematic representation of a nucleic acid terms should all be understood to include enzymatically aptamer-based microarray of binary probes. active portions thereof, whether they are produced syntheti FIG. 11 Is a schematic of a microarray of non-enzymatic cally or derived from organisms or other sources. The basic binary probes that selectively hybridize to a reporter oligo 10 probe has several distinct regions on each strand: an analyte nucleotide (RO) when the analyte-binding arms of the probe binding arm flanked by a flexible linker that is flanked by a hybridize to the target analyte. molecular beacon-binding arm that binds to a molecular bea DEFINITIONS con to indicate that the analyte has been detected. These 15 probes are called "binary" because the two parts of the probe A binary nucleic acid probe is a probe that is made of two act synergistically and the detection event occurs only when synthetic, non-naturally occurring, antiparallel oligonucle both strands are hybridized to the analyte. In the absence of a otide strands of DNA or RNA, or combinations or analogues nucleic acid analyte, the strands are dissociated and the probe thereof that act synergistically to detect a particular target does not detect the presence of the analyte. nucleic acid analyte in a complex sample. Each strand of the 20 (Deoxy)ribozymes or DNA/RNA enzymes or catalytic probe has an analyte-binding arm (ABA) that is complemen DNA or RNA are DNA or RNA molecules with catalytic tary to a portion of the particular target analyte. When the action. These molecules can bind one or more than one sub ABA hybridize to the target, causing the two strands of the strates and chemically transform them. probe to self assemble to generate a detectable signal indicat An aptamer is an RNA or DNA molecular that can specifi- ing the presence of the target analyte in the sample. In the 25 cally bind a specific target molecule. Aptamers are usually absence of a nucleic acid analyte, the strands are dissociated created by selecting them from a large random sequence pool. and no signal is generated. As used herein, the term "physi Reporter Oligonucleotide means an oligonucleotide to ologic conditions" is meant to suggest reaction conditions which a reporter molecule is linked, such as a gold nanopar emulating those found in mammalian organisms, particularly ticle, fluorescent molecule, quantum dot or any reporter that humans. While variables such as temperature, availability of 30 can be detected. In some embodiments the nonenzymatic cations, and pH ranges may vary. "Physiologic conditions" probes have a reporter oligonucleotide-binding arm that is generally mean a temperature of about 35-40° C., with 37° C. complementary to and hybridizes to the RO thereby generat being particularly preferred, and a pH of about 7 .0-8.0, with ing a detectable signal. The reporter molecule is any molecule 7 .5 being particularly preferred. The conditions also include that can be detected by optical, electrical or magneto electri- the availability of cations, preferably divalent and/or monova 35 cal means. lent cations, with a concentration of about 2-15 mM Mg2+ As used herein, the term "base pair" (bp) is generally used and 0 1.0 M Na+ being particularly preferred. to describe a partnership of adenine (A) with thymine (T) or "Nucleotide" generally refers to a monomeric unit of DNA uracil (U), or of cytosine (C) with guanine (G), although it or RNA consisting of a sugar moiety (pentose ), a phosphate should be appreciated that less-common analogs of the bases group, and a nitrogenous heterocyclic base. The base is linked 40 A, T, C, and G (as well as U) may occasionally participate in to the sugar moiety via the glycosidic carbon (1' carbon of the base pairings. Nucleotides that normally pair up when DNA pentose) and that combination of base and sugar is a "nucleo or RNA adopts a double stranded configuration may also be side". When the nucleoside contains a phosphate group referred to herein as "complementary bases". bonded to the 3' or 5' position of the pentose, it is referred to "Complementary nucleotide sequence" here generally as a nucleotide. A sequence of nucleotides is typically 45 refers to a sequence of nucleotides in a single-stranded mol referred to herein as a "base sequence" or "nucleotide ecule or segment of DNA or RNA that is sufficiently comple sequence", and their grammatical equivalents, and is repre mentary to that on another single oligonucleotide strand to sented herein by a formula whose left to right orientation is in specifically hybridize to it with consequent hydrogen bond the conventional direction of 5'-terminus to 3'-terminus, ing. Where single nucleotide polymorphisms are the target unless otherwise specified. 50 for detection, then the complementarity between the analyte In various embodiments, the binary probe of the present and analyte-binding arm on the binary probes should be invention may combine one or more modifications or muta exact, 100%. If less selectivity is required, then routine tions including additions, deletions, and substitutions. These experimentation will determine the level of complementarity mutations may, for example, change the length of, or alter the that provides the desired result. nucleotide sequence of, a loop, a spacer region or a recogni- 55 "Nucleotide analog" generally refers to a purine or pyri- ti on sequence (or domain). Modification or mutation of the midine nucleotide that differs structurally from A, T, G, C, or recognition site via well-known methods allows one to alter U, but is sufficiently similar to substitute for the normal the sequence specificity of an enzymatic nucleic acid mol nucleotide in a nucleic acid molecule. As used herein, the ecule. The oligonucleotide strands of the probe may contain term "nucleotide analog" encompasses altered bases, differ- one or more substitutions such as analogues, derivatives, 60 ent or unusual sugars (i.e. sugars other than the "usual" pen modified or altered bases, ribonucleotides, alterations of the tose), or a combination of the two. Nucleotide analogs of sugar or phosphate backbone, or any combination of these, DNA or RNA can be used to make binary probes. Examples well known to those skilled in the art of nucleotide analogs useful according to the present inven As used herein, the terms "deoxyribozyme" and tion include those listed in the approved listing of modified "ribozyme" are used to describe a DNA or RNA-containing 65 bases at 37 CFR .sctn.1.822 (which is incorporated herein by nucleic acid that is capable of functioning as an enzyme. In reference). Other useful analogs include those described in the present disclosure, the term "deoxyribozyme" and published international application no. WO 92/20823 (the US 8,853,134 B2 5 6 disclosures ofwhich are incorporated herein by reference), or a microarray. In other embodiments more than one substrate analogs made according to the methods disclosed therein. may be used depending on how the binary pro bes are custom "Oligonucleotide or polynucleotide" generally refers to a ized. In some embodiments a unique substrate may be needed polymer of single-stranded nucleotides. As used herein, "oli to detect each of several different target analytes. PCT Appli gonucleotide" and its grammatical equivalents will include cation PCT/US07/61583, Kolpashchikov D. M. (2007) the full range of nucleic acids. An oligonucleotide will typi ChemBioChem, 8, 2039-2042; Todd et al., U.S. Ser. No. cally refer to a nucleic acid molecule comprised of a linear 11/544,926 (20070231810), and in E. Mokany, et al., J. Am. strand of deoxy- and ribonucleotides. Chem. Soc. 2010, 132 (3), pp 1051-1059. A nucleic acidmicroarray is a multiplex technology used in In some embodiments the microarray includes binary non- molecular biology that consists of an arrayed series of up to 10 enzymatic probes, designed to selectively bind to a molecular thousands of microscopic spots of DNA or RNA or DNA/ beacon or a dye (through molecular beacon-binding arms or RNA chimeric oligonucleotides, called features, each con dye-binding arms, respectively) or to a reporter oligonucle taining picomoles of a specific nucleic acid sequence. otide bound to any detectable molecule (such as a quantum dot, gold nanoparticle is bound) thereby generating a detect- DETAILED DESCRIPTION 15 able signal when the analyte-binding arms on each strand hybridize to the particular target nucleic acid analyte. PCT It is to be understood at the outset, that the figures and Application PCT/US2007/065744, Kolpashchikov D. M. examples provided herein are to exemplify, and not to limit (2006) JACS, 128, 10625-10628; and Kolpashchikov D. M. the invention and its various embodiments. (2005) JACS, 127, 12442-12443. The present invention is directed to microarrays of binary 20 In other embodiments the microarray includes binary nucleic acid probes for the detection of one or a plurality of probes that have peroxidase-like activity that produce a vis nucleic acid analytes in a complex sample in a single high ible signal when complexed to the target analyte. When both throughput assay with extraordinary specificity under physi of the analyte-binding arms bind a target analyte, the two ologic conditions. Any binary nucleic acid probes that gen strands of the probe form a hemin-binding complex. Hemin erate a detectable signal when bound to analyte are suitable 25 has peroxidase activity that can be visualized by adding the for use in the microarrays, including binary deoxyribozyme appropriate substrate to generate a colored product indicating or ribozyme probes; nonenzymatic binary probes for fluores that the analyte has been detected. U.S. Provisional applica cent detection, nonenzymatic binary dye-binding probes, and tion 61/117,081, PCT Application PCT/US09/65341 and binary split enzyme peroxidase probes for visual detection of Kolpashchikov D. M. (2008) JACS, 130, 2934-2935. nucleic acids. Certain embodiments are also directed to non 30 The binary probes are sensitive to even a single nucleotide nonenzymatic binary probes that bind to reporter oligonucle mismatch, which destabilizes the probe preventing the two otides: halves of the pro be from hybridizing to the analyte to generate Binary probes and the microarrays to which they are bound a signal. As was reported earlier, the binary probes provide have the following advantages in comparison to the conven unprecedented selective recognition of 20 nucleotide long tional microarrays of liner DNA probes. (i) improved selec 35 targets (that can be part of an even longer nucleotide) at room tivity of SNP detection (low level of false positive signals), temperature, thus avoiding the need for the precise tempera (ii) avoid the need for the precise temperature control during ture control for SNP typing. The array of binary probes is an hybridization as the reactions can be conducted at ambient extremely efficient tool for pathogen and SNP analysis and temperatures, (iii) improved sensitivity due to catalytic may revolutionize DNA microarray technique. Sequence amplification of the positive signal, (iv) simplified readout 40 variations capable of detection by the microarrays of the procedure: in some formats the signal may be detected by present invention include, but are not limited to, additions, naked eye and/or by a conventional scanner, and (v) low cost: deletions, substitutions, conversions, duplications, transloca there will be no requirement fortarget labeling; the probes are tions, frame-shift sequence variants, nonsense sequence vari affordable synthetic oligodeoxyribonucleotides. ants, or any combination thereof. Reactions can be performed Binary nucleic acid probes have two synthetic, non-natu 45 over a wide range of temperatures, as long as the probes rally occurring, antiparallel oligonucleotide strands made of function as intended to generate the signal upon hybridization DNA or RNA, and combinations or analogues thereof that act to analyte. Because the probes discriminate between fully synergistically to detect a target nucleic acid analyte in a matched nucleic acid sequences and those containing mis complex sample. Each strand of the probe has an analyte matches, they can be used for the detection, identification and binding arm (ABA) that is complementary to and hybridizes 50 quantification of methylated nucleic acid. Abnormal methy with a portion of a specific target analyte, causing the two lation pattern occur frequently in association with diseases strands of the probe to self assemble to generate a detectable such as cancer, diabetes, autoimmune diseases, and psychi signal indicating the presence of the target analyte in the atric disorders. sample. In the absence of a nucleic acid analyte, the strands Immobilizing Binary Probes on a Microarray are dissociated and no signal is generated. 55 There are several ways in which the binary probe microar- Any binary probe can be used in the microarrays. In some rays can be created. In certain embodiments either one or both embodiments the microarray includes binary enzymatic strands of the binary probe are immobilized on a solid sup nucleic acid probe, wherein each strand of the probe has part port. In embodiments where both strands are immobilized, of the catalytic core of the enzyme that is reconstituted when the two strands of the binary probe are linked to one another the ABA on the two strands of the probe hybridize to the 60 through a flexible linker that permits each strand to hybridize analyte, restoring the catalytic activity of the enzyme and to the target analyte thereby generating a detectable signal. enabling it to bind to a substrate through substrate-binding The linker joining two strands of a binary probe is labeled arms on each strand and cleave the substrate, which in turn "linker 2" in the figures. When the two strands are linked, the generates a detectable signal, such as a fluorescent signal or a resulting molecule is herein referred to as a "binary probe color change (in the case of peroxidase). In some embodi 65 complex" and microarrays on which such complexes are ments the microarray is designed so that a single substrate is immobilized are referred to as "binary probe complex adequate for the plurality of different probes immobilized on microarrays. US 8,853,134 B2 7 8 In one embodiment, the two strands of the probe are bound activated only when the two strands bind to the target analyte to each other via an interstrand linker to make the binary reconstituting the catalytic core. The activated enzyme then probe complex. In another embodiment the binary probe cleaves the bound substrate generating a signal localized to complex is formed by joining the ends of the two strands the corresponding feature. In a preferred embodiment the opposite the analyte-binding arm (ABA) through an intras fluorescent end of the substrate remains immobilized on the trand linker to form a single oligonucleotide that comprises microarray and the quencher is released into solution upon both strands, leaving the ABA are free to bind to analyte as cleavage. If the probe is nonenzymatic, the bound molecule shown in FIG. 1. The plurality of binary probe complexes are can be a dye or molecular beacon that generates a signal only immobilized at a particular spot on the microarray through when the respective dye-binding or molecular beacon-bind another tethering linker (labeled "linker 1" in the figures) that 1 o ing arms hybridize to target analyte. can bind to any location on the complex as long as it does not In preferred embodiments a microarray is provided on interfere with target binding or signal generation. The tether which a plurality of binary probe complexes and/or single ing linker is itself covalently bound to the array; many such strands of the plurality ofbinary probes that detect a plurality linkers are well known in the art. Both linkers are preferably of nucleic acid analytes are immobilized at different sites on flexible linkers that permit the two halves of the probe to form 15 a solid support to create features. A single microarray can a double helix when bound to analyte. include features that comprise 1.) binary probe complexes in An embodiment in which the microarray features are made which the two strands are linked at an interstrand site, or 2.) by joining the two strands of the binary enzymatic probe to binary probe complexes in which the two strands are linked at one another via an intrastrand linker to make a single oligo an intrastrand site to form a single long oligonucleotide, or 3.) nucleotide or binary, probe complex. In the example shown in 20 only one strand of a probe immobilized to create a feature FIG. lA a linker (Linker 1) joins the two strands through the wherein the other strand is added separately, or 4.) the signal- substrate-binding arms on each strand, leaving the analyte generating molecule is immobilized on the support, or 5.) binding arms free to bind to the analyte. In the absence of a combinations of these. Moreover the binary probes them nucleic acid analyte the catalytic core remains deactivated selves can be of any type, enzymatic or nonenzymatic. Since due to the weak interactions between the two halves. Hybrid- 25 hybridization can be accomplished at physiologic conditions ization of each analyte-binding arm of the probe to a target it is possible to put different types of binary probes on the analyte stabilizes the structure of the core (FIG. lB) thereby same microarray, for example, mixing enzymatic and nonen forming an active enzyme. If a fluorogenic substrate is added zymatic probes, or different types of each. The target nucleic that is complementary to and hybridizes with the substrate acid analyte is added to the microrray under any conditions binding arm on each strand, the enzyme will cleave the fluo- 30 that permit it to selectively hybridize with the corresponding rogenic substrate. The quencher will dissociate in solution analyte-binding arms on the respective binary probe, thereby and the fluorophore will emit high fluorescence (FIG. lC). permitting the two strands of the probe to hybridize which Alternatively, the microarray feature can be made by generates a detectable signal indicating analyte-binding. immobilizing only one strand of the binary enzymatic probe In standard microarrays, the probes are attached to a solid (half of the probe) on the solid support. In the example shown 35 surface by a covalent bond to a chemical matrix (via epoxy in FIG. 2A a linker (Linker 1) is bound to the free end of the silane, amino-silane, lysine, polyacrylamide or others) or the analyte-binding arm on a first oligonucleotide strand of a solid surface can be glass, a silicon or an organic polymer binary deoxyribozyme probe. The second oligonucleotide chip. Many types of solid supports/surfaces are known in the strand ofthe probe is provided separately. In one embodiment art. In certain preferred embodiments, the support can be a the second strand of the probe is mixed with the target analyte 40 plastic material, such as plastic beads or wafers, or that of the under conditions that permit the analyte to hybridize to the well or tube in which a particular assay is conducted. The analyte-binding arm on the second strand to form an analyte/ immobilized probes complex creates what is called a feature strandhybridas is shown in FIG. 2B. The hybrid is thenadded on the microarray. Any method or linker that tethers a strand to the microarray under conditions that permit a portion of the of the binary probe to the support can be used, including any target analyte to bind to the analyte-binding arm on the first 45 methods that may involve noncovalent linkages, as long as the strand that is immobilized on the solid support, thereby form strand remains immobilized during the assay. Embodiments ing a complex that activates the enzyme. In another embodi ofthe present invention encompassing an insoluble support in ment the analyte can be added to the microarray onto which the form of an array or microarray called a "chip," typically the first strand is immobilized either before, together with or comprise a plurality of probes that are positioned upon the after adding the second strand. The appropriate substrate is 50 chip by any suitable method known in the art, for example, by added to the mixture at any time. The substrate then binds to pipette, ink-jet printing, contact printing or photo lithography. the substrate-binding arms on the first and second strand of The microarray/chip may have one or more features that may the probe/analyte complex, and it is cleaved by the activated be spaced apart at a uniform or a variable distance, or a enzyme thereby generating a detectable signal indicating the combination thereof. In some embodiments, the features may presence of the target analyte and its binding to the probe. 55 be positioned randomly, with the respective location of each FIG. 2C. element then determined. The size and shape of the features Routine experimentation will determine the optimum con will vary according to the intended use, and different sized ditions and timing for adding the various components neces and shaped features may be combined into a single microar sary for detecting the analyte in the complex sample. Any ray/chip. The surface of the microarray/chip may be substan- technique can be used as long as it permits the specific bind 60 tially planar or may have uneven topography such as depres ing of analyte to the ABA and generation of a detectable sions or protuberances. The features may be positioned either signal. into the depressions or onto the protuberances. Such depres In another embodiment of the microarray the molecule sions may provide a reservoir for solutions into which the generating the detectable signal is bound to the support and features are immersed, or they may facilitate drying of the the binary probe is added separately, either as two free 65 elements. For example, the features may be placed in each strands, or as a binary probe complex wherein the two strands well of a 96 well plate. In some embodiments, the microarray/ are linked. In the case of an enzymatic probe, the enzyme is chip may include unique identifiers such as indicia, radio US 8,853,134 B2 9 10 frequency tags, integrated devices such as microprocessors, made of RNA oligoribonucleotides, U is substituted for T; barcodes or other markings in order to identify each of the otherwise the structures are the same. elements. The unique identifiers may additionally or alterna- Typically only two short DNA, RNA, chimeric or oligo- tively comprise the depressions or protuberances on the sur- nucleotides need to be synthesized for each type ofprobe. The face of the array. The unique identifiers can provide for cor- 5 specific analyte-binding arms for each different probe have to rect orientation or identification of the microarray/chip and be customized. Standard desalting provides sufficient purity they may be read directly by a data capture device or by an for the oligonucleotides of such lengths. All other compo- optical scanner or detector. nents of the pro be, such as the substrates for enzymatic probes Binary Probe Structure or double labeled fluorescent molecular beacons, or the dyes The arms of any of the binary probes (such as the sub- 10 are universal. strate-, dye- or MB-binding arms, catalytic core and analyte- In general, for all types of binary probes, analyte-binding binding arms) are "linked" to one another typically through arms of 10 nucleotides are preferred because a combined phosphodiester bonds between the nucleotides at the ends of length of20 nucleotides will cover any unique sequence in the each respective arm, without adding additional linkers. How- genome. It is important to note, that the analyte itself can be ever, in some embodiments one or more separate linker mo!- 15 of any length from 12-40, to many thousand nucleotides. ecules are added between one or more arms of the probe. Any Additional changes that may increase the selectivity of the separate linkers added to the probe strands to join the parts or probe include shortening the analyte, for example from 20 to arms of the probe on each strand to one another can be used as 12 nucleotides, or increasing the reaction temperature. Since long as they are flexible enough to permit the probe to gen- the oligonucleotide strands of the binary probe are simple erate a detectable signal when theABA bind to the analyte. In 20 nucleotide sequences they can be made to order by various some cases the ABA will form a double or triple helix when existing companies such as Integrated DNA Technologies bound to analyte. In one example embodiment the ABA are (Coralville, Iowa, USA). homopyrimidine (alternating C and T, such as CCCTTTC- The basic structure of all of the binary probes can be CCCCCCTTTT) or homopurine (such as GGGAAAGGGG- modified. One modification includes adding a stem or probe- GAGAGA) sequences. Flexible linkers are generally pre- 25 binding arm, for example between the substrate-binding arm ferred. Binary RNA probes also form double helices. In and the catalytic core (or between the catalytic core and the certain embodiments the added linkers are nucleic acids, typi- ABA) on each strand of deoxyribozyme or ribozyme probes. cally from about 0 to about 3 nucleotides long, though longer The probe-binding arm provides a stem-loop type structure to linkers can be used (FIG. 6; "tt" is an added dinucleotide the probe and can add additional structural stability that in linker), or a non-nucleotide linker such as triethylene glycol 30 some cases enhance catalytic activity. can be used (FIG. 7). Hexa-ethyleneglycol provided for In another embodiment a nucleotide fragment of from example by Integrated DNA Technologies (Coralville, Iowa, about 0-40 nucleotides in length (preferably 1-10) called a USA) can also be used although this would substantially structure stabilization arm (SSA) is added to the free end of increase the cost of the probe. The length and sequence of the the analyte-binding arm on each strand of a probe to increase linkers between the various arms can also vary. Due to steric 35 sensitivity and stability of the probes. The added sequences in considerations pyrimidines are favored over purines when the SSA are complementary to all or part of the analyte- used as linker bases. Therefore in certain embodiments binding arm. When the complementary sequences in the SSA probes such as T, TT, TTT, C, CC, CCC linkers are preferred. hybridize to the corresponding sequences in the analyte-bind- In some embodiments the linker can be a short nucleotide ing arm, a stem-loop is formed. The formation of stem-loops such as a dinucleotide uracil bridge. Routine experimentation 40 represents a conformational constraint that further increases will determine the optimum probe design providing the high- the sensitivity of the binary DNA or RNA probes. SSA can est specificity and in the case of enzymatic probes, the highest also be added to the free end of the hemin-binding arm on rate of substrate cleavage in the presence of a DNA or RNA peroxidase-like probes if they do not interfere with g-com- analyte with the lowest background. Additional examples of plex formation. When the strands of the probe are present free flexible linkers are demonstrated in Example 4. It is not nee- 45 in solution, i.e., not hybridized to analyte, each dissociated essary that the linkers on each strand be identical, as long as strand of the probe is stabilized by complementary base pair- they permit the ABA to bind to the analyte and generate the ing to itself via the stem loop in the analyte-binding arms. detectable signal. The length and sequence of the various This self-complementary pairing results in a "hairpin loop" components of the binary nonenzymatic probes can be varied structure for the individual strands, which stabilizes the ali- as is described in PCT Serial No. PCT/US07/61583, PCT/ 50 gonucleotide strands and increases sensitivity. Certain pre US2007 /0657 44, and 61/117 ,081 to customize the probe for ferred embodiments of the invention are therefore directed to a particular analyte and optimize the reactions. the binary oligonucleotide probes where each strand of the All of the binary probes for use in the present invention can probe forms a stem loop structure when the strand is not be made of DNA, RNA, 2'-0-methyl RNA, locked nucleic hybridized to analyte. When analytes are 16 nucleotides long acids (LNA), or peptide nucleic acids (PNA) or any other 55 or shorter, adding stem-loops to the analyte-binding arms nucleic acid analogues that can form double and triple helixes may not be helpful. The size of the SSA will depend on the with nucleic acids or they can be a chimera. Likewise the size ofthe analyte and the type of reporter (dye or MB), which analyte can be DNA, RNA or a chimera. Since DNA-RNA will vary. It was discovered that sensitivity to a single mis and DNA-DNA hybrids have different structural parameters, match or single nucleotide polymorphism in analytes 20 the binary constructions should be customized for RNA in 60 nucleotides long increased if each strand of the probe was order to obtain highly specific and sensitive recognition of designed to form a stem-loop hairpin structure when not RNA targets. DNA probes have an advantage over RNA bound to analyte. probes when the analyte is DNA because DNA-DNA Certain other embodiments of the invention are directed to duplexes are typically less stable than RNA-DNA duplexes microarrays on which truncated forms of the probes as are and are therefore more sensitive to SNPs. DNA probes are 65 bound or provided in solution. An example of a truncated cheaper also to synthesize and they are more stable to degra binary deoxyribozyme probe is a probe each strand of which dation in solution. In those embodiments where the probes are has only substrate-binding arms and a portion of the catalytic US 8,853,134 B2 11 12 core. Users can customize the other regions of the probe, be increased if multiple substrate molecules cleavable by the adding for example ABA for any intended target analyte. reconstituted enzyme are added. Binary enzymatic probes include any binary deoxyri Different variations on the hemin-binding arm of the pro be bozyme, ribozyme or chimeric probes. Each oligonucleotide can be made. Some variations include the following. In one strand of a binary enzymatic probe has a substrate-binding 5 embodiment, the oligonucleotide hemin-binding arm on the arm (that binds the enzyme substrate such as a fluorescent first oligonucleotide strand includes the sequence 3' gggatggg substrate), (roughly) half of the catalytic core of the enzyme 5, and the oligonucleotide hemin-binding arm on the second and an analyte-binding arm. In some embodiments the probe oligonucleotide strand includes 5' gggttggg 3'. In other includes an optional probe-binding arm that lends structural embodiments the oligonucleotide hemin-binding arm on the stability to the probe and may improve enzymatic activity. 10 first oligonucleotide strand comprises 3' ggg 5; and the oli (FIG. 5). In some embodiments, the oligonucleotide strands gonucleotide hemin-binding arm on the second oligonucle of binary enzymatic and nonenzymatic probes have optional otide strand comprises 5' gggcgggttggg 3', or the oligonucle structure stabilization arms that are linked to the analyte otide hemin-binding arm on the first oligonucleotide strand binding arms, and that provide structural stability and mini comprises 3' gggcgggatggg 5; and the oligonucleotidehemin mize nonspecific binding to analyte. A large variety of 15 binding arm on the second oligonucleotide strand comprises reporter substrates including fluorophores and quenchers can 5' ggg 3'. See FIG. 3 and FIG. 7. be used in enzymatic probes (such as FAM, TET, TAMRA Nonenzymatic binary DNA probes (BDP) for use in the and others known in the art, and quenchers (such as Dabcyl, present invention [Kolpashchikov D. M. (2006) JACS, 128, TAMRA, Iowa Black™, Black Hole Quencher®-!, Black 10625-10628] bind to molecular beacons or dyes to generate Hole Quencher®-2) are commercially available (IDT Inc.). 20 a signal. Each antiparallel strand has a MB- or dye-binding An example of a microarray feature in which the binary arm and an analyte-binding arm, with an optional stem probe is a peroxidase DNA enzyme is shown in FIG. 3. between these two arms. Alternatively the MB- or dye-bind Provisional application 61/117081, PCT Application PCT/ ing arms and the ABA on each strand are linked by an added US09/65341 and Kolpashchikov D. M. (2008) JACS, 130, linker such as triethylene glycol. FIG. 4 and FIG. 8. The MB 2934-2935. In this embodiment, each strand peroxidase 25 and dye-binding arms are designed to be complementary to probe has a customized fragment that is complementary to a and hybridize with nucleotide fragments or sequences in any selected target nucleic acid analyte (analyte-binding arm), molecular beacon or dye known in the art. A molecular bea and a customized fragment complementary to hemin (hemin con (MB) is a fluorophore- and a quencher-conjugated DNA binding arms). While the ABA on a peroxidase-like pro be can or RNA hairpin. The probe can be customized for any fluo be DNA, RNA or chimeras, the hemin-binding arms are only 30 rophore, including FAM, TAMRA, Dy 750, HEX™, JOE, made of DNA. In the embodiment shown in FIG. 7, analyte TET™, Texas Red-X, Alexa Fluor. Dyes, Bodipy Dyes, CY and hemin-binding arms are connected to each other by added Dyes, Rhodamine, dyes, WellRED Dyes, MAX, and TEX non-nucleotide linker molecules. When both of the analyte 613; and for any quencher including black hole quenchers binding arms bind a target analyte, the two strands of the (BHQl, BHQ2, BHQ3), Iowa Black Quenchers, and DAB probe bind hemin which has peroxidase activity that can be 35 CYL. visualized by adding the appropriate substrate to generate a Molecular beacon-binding arms on each strand are typi colored product indicating that the analyte has been detected. cally 3-20 nucleotides long, but routine experimentation In the example shown in FIG. 3, each half of the binary based on the molecular beacon will determine the optimum peroxidase-like probe contains a fragment (alpha and beta) of length. FIG. 8. The molecular beacon-binding arms need to the catalytic core of the DNA peroxidase enzyme, and only 40 be long enough to separate the fluorophore on the MB from one strand is immobilized on the surface ofthe array by linker the quencher to facilitate fluorescence only when the molecu 1 (FIG. 3B). This fragment is unable to form catalytic com lar beacon is bound to the probe. Although most molecular plex with hemin until the ABA on both the first second strands beacons are DNA oligonucleotides, there is no technical hybridize to target analyte. In this embodiment, the second obstacle to making molecular beacons that are RNA or chi strand of the probe is mixed with the target analyte in solution 45 meras of DNA and RNA for use in the new binary RNA permitting the analyte to bind to the analyte-binding arm on oligonucleotide probes. Specific examples of binary molecu the second strand to form a hybrid (FIG. 3C). The second lar beacon- or dye-binding probes are described in our earlier strand/analyte hybrid is then mixed/incubated with the array work, PCT/US2007/065744, incorporated herein by refer under conditions that permit the ABA on the immobilized first ence, (See Also: Tyagi, S., Kramer, F. R. 1996. Molecular strand to bind to the target analyte, thereby bringing the two 50 beacons: probes that fluoresce upon hybridization. Nat. Bio halves of the probe together to form a hemin-binding G-qua technol. 14: 303-308. 10. Bonnet, G., Tyagi, S., Libchaber,A., druplex from the combined alpha and beta fragments. (FIG. Kramer, F. R. 1999. Thermodynamic basis of the enhanced 3D) Hemin catalyzes degradation of hydrogen peroxide and specificity of structured DNA probes. Proc. Natl. Acad. Sci. the products of peroxidase degradation in tum oxidize a num U.S.A. 96: 6171-6176. 11. Marras, S.A., Tyagi, S., Kramer, F. ber of different substrates including DAB (3,3'-diaminoben- 55 R. 2006. Real-time assays with molecular beacons and other zidine) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic fluorescent nucleic acid hybridization probes Clin. Chim. acid) (ABTS). Any substrate that can be hydrolyzed by per Acta. 363: 48-60.) oxidase can be used. The substrate oxidation products are Where dye-binding probes are used, there is a measurable water insoluble and stain the microarray feature (brown in the change in dye properties (for example fluorescence, phospho case of DAB) (FIG. 3E), which can be detected either by a 60 rescence or electronic spectra) upon binding to analyte, which scanner or visually (in microscope in the case if the feature is easily and instantly detectable. In one embodiment the size in the range of micrometers). The active hemin-binding binary dye-binding probe is an unmodified RNA oligonucle probe will not be formed if the analyte has even one non otide malachite green aptamer (MGA). An aptamer is a type complementary nucleotide, thus enabling the arrays to be of synthetic oligonucleotide that can bind to a particular target used for SNP detection. If a substrate such as luminal is used 65 molecule, in this case a molecule is capable of generating a as an oxidizable substrate instead of DAB, a chemilumines detectable signal. FIG. 10. Is a schematic representation of a cent signal will be generated. The sensitivity of the probe can nucleic acid aptamer-based microarray of binary probes. The US 8,853,134 B2 13 14 MGA is an RNA molecule that has submicromolar affinity to acid profiles of the prepared probes and is ready to receive malachite green (MG), a triphenylmethane dye. Upon bind complementary nucleic acid analyte "targets" derived from ing to analyte, MGA increases the fluorescence of the experimental or clinical samples. These arrays may be easily dye >2000 fold. (Babendure, J. R., J. Am. Chem. Soc. 2003, customized for each experiment, because researchers can 125, 9266-9270), incorporated herein by reference. When the choose the probes and printing locations on the arrays, syn target nucleic acid hybridizes to the analyte-binding arms, the thesize the probes in their own lab (or collaborating facility), probe binds to the MG dye and a detectable fluorescent signal and spot the arrays. is generated. See FIG. 9. Other aptamers that can be modified It is possible to make certain microarrays of binary probes for use as a binary dye probe include a modified sul as an "oligonucleotide array," referring to a specific technique forodamine B aptamer (for the probe), and a sulforodamine 10 of manufacturing. Oligonucleotide arrays are produced by dye, including but not limited to patent blue violet or patent printing short oligonucleotide sequences or synthesizing the blue VF. Other dyes that come within the scope of the inven sequences directly onto the array surface instead of deposit tion include triphenylmethane dyes like malachite green, ing intact sequences. Sequences may be up to 60-mer probes including bis (N-methylindoliny), and Malichite Green IMG. depending on the desired purpose. Shorter probes such as Certain embodiments of the invention are drawn to new 15 those in the binary probes may be spotted in higher density binary reporter oligonucleotide probes that can also be used across the array and are cheaper to manufacture. in the new microarrays. Reporter Oligonucleotide (RO) The photolithographic synthesis of microarrays (such as is means an oligonucleotide to which a reporter molecule is used by Agilent and Affymetrix) is done on a silica substrate linked, such as a gold nanoparticle, fluorescent molecule, where light and light-sensitive masking agents are used to quantum dot or any reporter that can be detected. Each anti 20 "build" a sequence one nucleotide at a time across the entire parallel strand of binary reporter oligonucleotide probes have array. Each applicable probe is selectively "unmasked" prior a reporter oligonucleotide-binding arm that is complemen to bathing the array in a solution of a single nucleotide, then tary to and hybridizes to a portion of the RO, and analyte a masking reaction takes place and the next set of probes are binding arms. RO probes optionally have substrate stabiliza unmasked in preparation for a different nucleotide exposure. tion arms, and stem regions. The RO-binding arms and the 25 After many repetitions, the sequences of every probe become ABA are either linked by phosphodiester bonds between fully constructed. Any method known in the mart for making nucleotides at the joined ends, or by added linkers that can be the arrays and immobilizing one or both halves of the binary nucleotide or nonnucleotide, as described herein. The RO probes on the array can be used in the present invention. probes generate a detectable signal only when the ABA bind Kits to target analyte. RO probes optional have substrate stabili- 30 In an embodiment the microarray is provided as a kit that zation arms and linkers as described herein. In some embodi- includes a solid support on which the first strands of a plural ments the RO sequence is independent of the analyte ity of binary probes are fixed to particular known sites on the sequence: this enables using only one universal reporter mol microarray, and the respective second strands are provided ecule for analysis of almost any RNA/DNA analyte, which separately. The kit optionally includes the appropriate reduces the cast of such assays. 35 reporter. Since the hybridization can take place at physiologic An example of SNP analysis using a nonenzymatic conditions, it is possible to put different types of binary molecular beacon-binding probe is shown in FIG. 4. In this probes on the same microarray, for example, mixing enzy embodiment the first strand of the probe is immobilized on a matic and nonenzymatic probes, or different types of each. support via a flexible linker to the analyte-binding arm (FIG. The present invention also provides kits for using the microar- 4A). The second strand of the probe is separate and hybrid 40 rays of the present invention. For example, in one embodi ized to the analyte in solution to form a hybrid (FIG. 4B). The ment a kit may comprise in a first container, a microarray of hybrid is then incubated with the support in the presence of features of immobilized binary probe complexes, and in a the complementary molecular beacon. Only in the case of second container the appropriate molecules needed to gener fully complementary analyte the fluorescent complex (FIG. ate a detectable signal when the probes bind the target analyte. 4C) is formed. A single mismatch prevents molecular beacon 45 Where the probes are enzymatic probes, the kit may further binding to the pro be, FIG. 4 D. Another embodiment of binary include the appropriate enzyme substrate or substrates. If dye-binding probe is Hoechst dye-binding aptamer devel peroxidase like probes are on the array, then the kit would oped by Sando et al. (Sando S, NaritaA,Aoyama Y. Light-up include hemin and for example DAB. Where the probes are Hoechst-DNA aptamer pair: generation of an aptamer-selec nonenzymatic, the kit may include the molecular beacons or tive fluorophore from a conventional DNA-staining dye 50 dyes to which the probes hybridize. If enzymatic and nonen Chembiochem. 2007 Oct. 15; 8(15):1795-803. zymatic probes are immobilized on the microarray, suitable Microarray Fabrication substrates forthe enzyme(s) and signal-generating molecular Microarrays can be fabricated using a variety of technolo beacons or dyes are included in the kit. In those embodiments gies, including printing with fine-pointed pins onto glass where only one strand of the plurality of binary probes are slides, photolithography using pre-made masks, photolithog 55 immobilized on the array, the kit would further include the raphy using dynamic micromirror devices, ink-jet printing or second strand of each of the plurality of immobilized probes electrochemistry on microelectrode arrays. Various methods in a separate container. In some embodiments the pro bes may for making microarrays on which nucleic acid probes are not have analyte-binding arms, which are added by the users. immobilized are well known in the art. Some are discussed in Typically, the kits of the present invention will also include Todd, et al., U.S. Ser. No. 11/544,926. 60 one or more other containers, containing for example, wash In spotted microarrays, the probes are oligonucleotides reagents, and/or other reagents as required in the performance probes are synthesized prior to deposition on the array surface of the methods of the invention. The kits may be compart and are then "spotted" onto glass. A common approach uti mentalized and may also include containers may allow the lizes an array of fine pins or needles controlled by a robotic efficient transfer of reagents from one compartment to arm that is dipped into wells containing DNA probes and then 65 another compartment without cross-contamination of the depositing each probe at designated locations on the array samples and reagents, and the addition of agents or solutions surface. The resulting "grid" of probes represents the nucleic of each container from one compartment to another in a US 8,853,134 B2 15 16 quantitative fashion. Such kits may also include a container the loading buffer (50% Glycerol, 50 mM HEPES, pH 7.4, 50 which will accept the test sample, a container which contains mM MgCl2 , 20 mM KC!, 120 mM NaCl, 0.03% Triton the reagents used in the assay, containers which contain wash X-100, 1%DMSO,0.01%bromphenol,0.01%xylencyanol). reagents, and containers which contain a detection reagent. Two micro liters of each sample can be loaded on the gel and Typically, a kit of the present invention will also include 5 run 1 hat room temperature (200V) followed by staining with instructions for using the kit components to conduct the SYBR Gold (Invitrogen, OR) and photographed using appropriate methods. Alphaimager 3400 (Alpha Innotech, CA). In embodiments where a binary peroxidase-like enzyme Substrates for Peroxidase Probes ABTS (2,2'-azino-bis(3- probe is immobilized on the microarray, the probes bind ethylbenzthiazoline-6-sulphonic acid) is a commonly used hemin from solution, which catalyzes the degradation of 10 water soluble substrate of hydrogen peroxidases. Therefore, hydrogen peroxide to products that in tum oxidize a number DAB can be substituted with ABTS in the colorimetric assay of different (secondary) substrates including DAB (3,3'-di for SNP. Addition of analyte should make the color of solu aminobenzidine) to water insoluble oxidation products that tion containing binary DNA peroxidase probe tum green; this stain the microarray feature in brown for visual detection. In color would be visually distinct from the solution containing this format the signal may be detected by naked eye and/or by 15 mismatched rs242557-A or no analyte. ABTS can replace a conventional seamier. Kits that include microarrays on DAB in the SNP typing assay, but with substantial reduction which one or both strands of a binary peroxidase-like probe ofS/B (from -10 to -6). are immobilized will also optionally include hemin, hydro Dithymidine Linkers Triethylene glycol linkers in the gen peroxide and the substrates that can be oxidized by the sequence of the binary DNA peroxidase probe are preferred. peroxidase reaction products. 20 Dithymidine linkers can be used, however, it is possible that in certain embodiments the intensity of the optical signal may EXAMPLES be reduced. We found that the signal was reduced about 6 times when dithymidine linkers were used with the peroxi In the following Examples the specificity of the binary dase-like probe described in a. above, generating a weak color probes for detecting a specific target nucleic acid analyte were 25 that was hardly recognizable by the naked eye (data not carried out in solution. The two oligonucleotide strands of the shown). At the same time, the probes composed of a~u and probe were not linked to one another and neither strand was au~ generated color intensive enough to be visualized in a test bound to a microarray, hereafter "free binary probes." A per tube. The highest signal-to-background ratios were found for son of skill in the art can adapt these protocols for use with the au~u and a~" combinations, -46 and-30, respectively, due microarrays of the present invention. 30 to a very low background reaction. In all cases the probes DNAse/RNAse free water was purchased from Fisher Sci were highly selective and generated no signal above the back entific Inc. (Pittsburgh, Pa.) and used for buffers, and for stock ground in the presence of the mismatched analyte in solution. solutions of oligonucleotides. Oligonucleotides were cus These data show that at least one strand of the probe can be tom-made by Integrated DNA Technologies, Inc. (Coralville, composed of purely natural nucleotides. The cost for chemi- Iowa) or by TriLink BioTechnologies, Inc (San Diego, 35 cal incorporation of dithymidine linker is almost 50 times Calif.). Fluorescent spectra can be taken on a Perkin-Elmer lower than that of the triethylene glycol linker. Therefore, (San Jose, Calif.) LS-55 Luminescence Spectrometer with a using a nucleotide linker may further reduce the assay cost. Hamamatsu Xenon lamp. Electronic spectra can be taken on a Spectrophotometer Ultraspec 3300 (Amersham-Biotech, Example 2 NJ, USA). The data can be processed using Microsoft Excel. 40 Nonenzymatic Binary Nucleic Acid Probes Example 1 Source of Molecular Beacons (MB) MBs are robust reagents for detecting and quantitating nucleic acids, even in Peroxidase-like Binary Probes real time (e.g., MBs can be used to detect targets as they are Details for making free binary oligonucleotide peroxidase 45 formed). A variety of commercial suppliers produce standard probes and for and testing them in solution for SNP analysis, and custom molecular beacons, including Chruachem (chru are set forth in U.S. Provisional Application 61/117,081. Oli achem.com), Oswel Research Products Ltd. (UK; oswel gonucleotides were custom-made by Integrated DNA Tech .com), Research Genetics (a division of Invitrogen, Hunts nologies, Inc. (Coralville, Iowa). Hydrogen peroxide, 3-3' ville, Ala. (resgen.com)), the Midland Certified Reagent diaminobenzidine tetrahydrochloride (DAB), 2,2'-azino-bis 50 Company (Midland, Tex. mere.com) and Gorilla Genomics, (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), hemin, LLC (Alameda, Calif.). A variety of kits which utilize and HEPES were from Sigma-Aldrich (St. Louis, Mo., USA). molecular beacons are also commercially available, such as B. SNP typing assay. The free binary peroxidase-like DNA the Sentinel™ Molecular Beacon Allelic Discrimination Kits enzymes (1 µM both strands) were incubated in the reaction from Stratagene (La Jolla, Calif.) and various kits from Euro- buffer (50 mM HEPES, pH 7.4, 50 mM MgCl2 , 20 mM KC!, 55 gentec SA (Belgium, eurogentec.com) and Isogen Bioscience 120 mM NaCl, 0.03% Triton X-100, 1% DMSO, hemin (125 BV (The Netherlands, isogen.com, the entire contents of nM), H2 0 2 (1 mM), and DAB or ABTS (1 mM)) in the which are hereby incorporated by reference as if fully set absence or presence of analyte . Negative control (sample 0) forth herein. would have no oligonucleotides. For SNP typing of free Binary Malachite Green-binding Probe probes in solution the electronic absorption spectra of the 60 A. Binary Malachite Green Aptamer probe. To test the samples were recorded after 30 min of incubation with the specificity of the probe, MG (2 µM) and two RNA strands of analyte at room temperature, and the test tubes were photo biMGA probe (1 µMeach) were mixed in 5.3 ml of the buffer graphed using Olympus FE-170 digital camera 6 mega pixels. containing 50 mM TrisHCI pH 7.4, 140 mM NaCl, 5 mM Native PAGE can be used to test the binary probes. The KC!, 1 mM MgCl2 . The free probes were incubated with reaction mixtures containing analyte bound to free peroxi- 65 analyte for 15 min at room temperature. Fluorescent spectra dase probe were analyzed in 12% native PAGE containing the were taken on a Perkin-Elmer (San Jose, Calif.) LS-55 Lumi- reaction buffer. Each reaction mixture can be mixed 1: 10 with nescence Spectrometer with a Hamamatsu Xenon lamp. US 8,853,134 B2 17 18 Experiments can be performed at the excitation wavelength -continued of 610 nm and emission scan of 620-720 nm. The emitting Int dSpacer intensities at 648 nM can be used for the calculation of the Structure discrimination factors. The data of four independent experi '5 ments were processed using Microsoft Excel. Example 4 \p Flexible Linkers The "Int" linkers below, referred to by the manufacturer Integrated DNA technology as "spacers" can be 10 0 used to make the probes of the present invention. I O=P-0 I Int C3 Spacer: 0 Structure ~3' 15 '5 ~o~o I In the foregoing specification, the invention has been O=P-0 described with reference to specific embodiments. It will, I however, be evident that various modifications and changes 0 20 ~3' may be made without departing from the broader spirit and Int Spacer 18 scope of the invention. The specification and drawings are, accordingly, to be regarded in an illustrative rather than a '5"1,,0 ~o~0 ~o~0~o) restrictive sense. The contents of all references, pending 25 patent applications and published patents, cited throughout 0 this application are hereby expressly incorporated by refer I O=P-0 ence as if set forth herein in their entirety, except where I o"l.i. terminology is not consistent with the definitions herein. 3' Although specific terms are employed, they are used as in the art unless otherwise indicated. SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS, 19 <210> SEQ ID NO 1 <211> LENGTH, 35 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic Sequence <400> SEQUENCE, 1 ctcttcagcg atcagttctt ctctctccat gagag 35 <210> SEQ ID NO 2 <211> LENGTH, 38 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 2 tgggtctcgc acccattgaa ctgcacccat gttagtga 38 <210> SEQ ID NO 3 <211> LENGTH, 15 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 3 gagaaggata tcact 15 US 8,853,134 B2 19 20 -continued <210> SEQ ID NO 4 <211> LENGTH, 20 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 4 atggagagag tgggtgcgag 20 <210> SEQ ID NO 5 <211> LENGTH, 17 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 5 gggtagggcg ggttggg 17 <210> SEQ ID NO <211> LENGTH, 8 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, gggtaggg 8 <210> SEQ ID NO 7 <211> LENGTH, 10 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 7 ccgtgtcctg 10 <210> SEQ ID NO 8 <211> LENGTH, 8 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 8 gggttggg 8 <210> SEQ ID NO 9 <211> LENGTH, 8 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 9 gtgcaccc 8 <210> SEQ ID NO 10 <211> LENGTH, 10 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence US 8,853,134 B2 21 22 -continued <400> SEQUENCE, 10 ccgtgtcctg 10 <210> SEQ ID NO 11 <211> LENGTH, 34 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 11 tggcttcgcc cagggtgcac caggacacgg tttt 34 <210> SEQ ID NO 12 <211> LENGTH, 15 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 12 ctctctccat gagag 15 <210> SEQ ID NO 13 <211> LENGTH, 15 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 13 tgggtctcgc accca 15 <210> SEQ ID NO 14 <211> LENGTH, 25 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 14 ccgagaagtt aagacctatg ctcgg 25 <210> SEQ ID NO 15 <211> LENGTH, 20 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 15 atggagagag tgggtgcgag 20 <210> SEQ ID NO 16 <211> LENGTH, 38 <212> TYPE, RNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 16 ggaucccgac uggcgagagc cagguaacga auggaucc 38 <210> SEQ ID NO 17 <211> LENGTH, 19 US 8,853,134 B2 23 24 -continued <212> TYPE, RNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 17 gcacccauuu cccgacugg 19 <210> SEQ ID NO 18 <211> LENGTH, 14 <212> TYPE, DNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic construct <400> SEQUENCE, 18 gagagagtgg gtgc 14 <210> SEQ ID NO 19 <211> LENGTH, 25 <212> TYPE, RNA <213> ORGANISM, Artificial Sequence <220> FEATURE, <223> OTHER INFORMATION, Synthetic sequence <400> SEQUENCE, 19 ccagguaacg aauggauucu cucuc 25 30 What is claimed: wherein the analyte binding arm of one strand of each of 1. A microarray for detecting a plurality of nucleic acid the plurality of binary probe complexes is covalently analytes in a complex sample, comprising a plurality of non bound to the solid support by a linker. naturally occurring binary nucleic acid probe complexes 2. The microarray of claim 1, wherein the two oligonucle- immobilized at separate sites on a solid support, wherein each 35 otide strands of the binary probe are bound to one another by a linker. complex comprises a binary nucleic acid probe comprising 3. The microarray of claim 1, wherein the binary probe two oligonucleotide strands that generate a detectable signal binds to a molecular beacon, dye or a labeled reporter oligo when each strand is bound to one of the plurality of analytes; nucleotide generating a fluorescent signal when both analyte- wherein the binary nucleic acid probe is a non-naturally 40 binding arms are bound to the analyte. occurring nonenzymatic reporter oligonucleotide-bind 4. The microarray as in claim 1, wherein the linker is a ing binary nucleic acid probe for detecting an oligo member selected from the group comprising epoxy-silane, nucleotide analyte comprising two oligonucleotide amino-silane, lysine, and polyacrylamide. strands wherein 1. a first oligonucleotide strand com 5. The microarray of claim 2, wherein first and second prises: a. at its 5'-terminus a reporter oligonucleotide oligonucleotide strands are linked to one another though a 45 linker that is a member of the group comprising T, C, dinucle binding arm that is complementary to and selectively otides including CC and TT, trinucleotides including TTT and hybridizes with a reporter oligonucleotide to which a CCC, oligoethylene glycol, hexa-ethyleneglycol and trieth reporter that can be detected is bound, and b. at its ylene glycol. 3'-terminus an analyte-binding arm that is complemen 6. The microarray of claim 1, wherein the solid support is tary to and selectively hybridizes with a first region of 50 a member selected from the group comprising an organic the oligonucleotide analyte, and 2. a second oligonucle polymer, glass, silicon, optical fiber, carbon nanotube, gold otide strand comprises: a. at its 3'-terminus a reporter nanoparticle, or gold covered surface of a sensor. oligonucleotide-binding arm that is complementary to 7. The microarray of claim 1, wherein the binary probe and selectively hybridizes with a reporter oligonucle binds to a labeled reporter oligonucleotide generating a signal otide to which a reporter that can be detected is bound, 55 that can be detected by optical, electrical or magneto electri and b. at its 5'-terminus, an analyte-binding arm that is cal means when both analyte-binding arms are bound to the complementary to and selectively hybridizes with a sec analyte. ond region of the oligonucleotide analyte; and * * * * *