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(12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin Et Al US 20100317005A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin et al. (43) Pub. Date: Dec. 16, 2010 (54) MODIFIED NUCLEOTIDES AND METHODS (22) Filed: Mar. 15, 2010 FOR MAKING AND USE SAME Related U.S. Application Data (63) Continuation of application No. 11/007,794, filed on Dec. 8, 2004, now abandoned, which is a continuation (75) Inventors: Susan H. Hardin, College Station, in-part of application No. 09/901,782, filed on Jul. 9, TX (US); Hongyi Wang, Pearland, 2001. TX (US); Brent A. Mulder, (60) Provisional application No. 60/527,909, filed on Dec. Sugarland, TX (US); Nathan K. 8, 2003, provisional application No. 60/216,594, filed Agnew, Richmond, TX (US); on Jul. 7, 2000. Tommie L. Lincecum, JR., Publication Classification Houston, TX (US) (51) Int. Cl. CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl. ............................................................ 435/6 LIFE TECHNOLOGES CORPORATION (57) ABSTRACT CFO INTELLEVATE Labeled nucleotide triphosphates are disclosed having a label P.O. BOX S2OSO bonded to the gamma phosphate of the nucleotide triphos MINNEAPOLIS, MN 55402 (US) phate. Methods for using the gamma phosphate labeled nucleotide are also disclosed where the gamma phosphate labeled nucleotide are used to attach the labeled gamma phos (73) Assignees: LIFE TECHNOLOGIES phate in a catalyzed (enzyme or man-made catalyst) reaction to a target biomolecule or to exchange a phosphate on a target CORPORATION, Carlsbad, CA biomolecule with a labeled gamme phosphate. Preferred tar (US); VISIGEN get biomolecules are DNAs, RNAs, DNA/RNAs, PNA, BIOTECHNOLOGIES, INC. polypeptide (e.g., proteins enzymes, protein, assemblages, etc.), Sugars and polysaccharides or mixed biomolecules hav ing two or more of DNAs, RNAs, DNA/RNAs, polypeptide, (21) Appl. No.: 12/724,392 Sugars and polysaccharides moieties. 6.OOE+04 5.OOE+04 4.00E+04 2 2 3.00E+04 B 2.OOE+04 1.OOE+04 OOOE+00 Patent Application Publication Dec. 16, 2010 Sheet 1 of 20 US 2010/0317005 A1 Patent Application Publication Dec. 16, 2010 Sheet 2 of 20 US 2010/0317005 A1 -e Patent Application Publication Dec. 16, 2010 Sheet 3 of 20 US 2010/0317005 A1 Patent Application Publication Dec. 16, 2010 Sheet 4 of 20 US 2010/0317005 A1 d.LN-T-L Patent Application Publication Dec. 16, 2010 Sheet 5 of 20 US 2010/0317005 A1 O-O-O-O-O-O-O-, +d.LN-T-L Patent Application Publication Dec. 16, 2010 Sheet 6 of 20 US 2010/0317005 A1 H : Patent Application Publication Dec. 16, 2010 Sheet 7 of 20 US 2010/0317005 A1 ATP-1-ROX ROX 0.40 AU O20 OOO 0.00 5.00 10.00 15.00 20.00 25.00 30.00 35.00 MINUTES O.30 AU 0.20 ATP-1-ROX ROX 0.10 0.00 OOO 5.00 10.00 15.00 20.00 25.00 30.00 35.00 MINUTES FIG. 5 Patent Application Publication Dec. 16, 2010 Sheet 8 of 20 US 2010/0317005 A1 0.40 0.35 O.30 0.25 AU O.20 O.15 O. 10 0.05 645.6 706.7 786.2 0.00 200.00 300.00 400.00 500.00 600.00 700.00 nm. FIG. 6 ATP/CAP ATP ATP EDAROX/CAP : ATP EDAROX Patent Application Publication Dec. 16, 2010 Sheet 9 of 20 US 2010/0317005 A1 d'OL doL-XOX)–> -OLI——> UBOSOL|- Patent Application Publication Dec. 16, 2010 Sheet 10 of 20 US 2010/0317005 A1 OOOC OOO O09 OO O OOOC OOO O09 OO O OOOC OOO O09 OO O n O h H X O n1 Patent Application Publication Dec. 16, 2010 Sheet 11 of 20 US 2010/0317005 A1 000|| 009 009 007 00Z UUL X LNO Patent Application Publication Dec. 16, 2010 Sheet 12 of 20 US 2010/0317005 A1 000Z09/..| 009 092 000|| 006 009 00/ 009 009 009 OOZ UUL X LNO Patent Application Publication Dec. 16, 2010 Sheet 13 of 20 US 2010/0317005 A1 T4 PNK 5' End-labeling TimeCourse With ATP-L1-ROX 0.5 1 3 6 18 (Hrs) FIG. 12A 1.OO O.75 Relative Activity O5O O.25 O.OO (-) 0.5 1 Time (Hrs) FIG. 12B Patent Application Publication Dec. 16, 2010 Sheet 14 of 20 US 2010/0317005 A1 T4 PNK Concentration Experiment 110 220 550 110 220 550 (uM) 10 Units 20 Units FIG. 13A 1.OO 0.75 % Activity % % 20 Units O.OO25 Y 3% 110 220 550 ATP-L1-ROX (uM) FIG. 13B Patent Application Publication Dec. 16, 2010 Sheet 15 of 20 US 2010/0317005 A1 5' End-Labeling Improvements with PEG 8000 1.00 0.75 Re. Activity O.50 O.25 O.OO 4% 6%. 8%. 12%. 18% PEG 8000 FIG. 14 Linker Effects on 5' End-labeling with ATP-Li-ROX Re Activity LinkerS FIG. 15A Patent Application Publication Dec. 16, 2010 Sheet 16 of 20 US 2010/0317005 A1 Linker Effects on 5' End-labeling with ATP-Li-FLU 1.00 Sas O.75 Re. Activity 0.50 O.25 1. O.OO FIG. 15B 5' ROX - 3' 3' - 5' A FIG. 1.6A Patent Application Publication Dec. 16, 2010 Sheet 17 of 20 US 2010/0317005 A1 5' ROX-oligonucleotide With duTP at 3' end 5' ROX-oligonucleotide -> . W. FIG. 16B ROX-Oligonucleotide-> Oligonucleotide FIG. 17A Patent Application Publication Dec. 16, 2010 Sheet 18 of 20 US 2010/0317005 A1 Dr. O >< ? Q) O C --> 75 CD (5 JC CD Z oligonucleotide –o?coºLo<?º? OCD CYYOS5È <[ ± >> |_ O V –1 IS NS JS 2.5 10 ?S Time (min.) FIG. 17B Patent Application Publication Dec. 16, 2010 Sheet 19 of 20 US 2010/0317005 A1 |T Patent Application Publication Dec. 16, 2010 Sheet 20 of 20 US 2010/0317005 A1 OSD ZeO OSD9 LeO OSD9 Wo OSD C.W.W g3. OSD9 WW OSD9 Wo 3 OSD OSD8 eO LeO Wo ZWW WW Wo OSD9 O) VN AISuelu 9 U US 2010/031 7005 A1 Dec. 16, 2010 MODIFIED NUCLEOTDES AND METHODS 0009. In addition to fluorescence, another important FOR MAKING AND USE SAME nucleic acid labeling method is the attachment of biotin to DNA or RNA. A variety of nucleic acid and protein capture RELATED APPLICATIONS applications are developed that exploit the highly specific interaction between biotin and streptavidin. 0001. The present invention claims provisional priority to 0010. As an example, magnetic column separations where U.S. Provisional Patent Application Ser. No. 60/527,909, biotinylated oligonucleotides are captured by Streptavidin filed 8 Dec. 2003 and is a Continuation-in-part of U.S. patent coated microbeads enable a straightforward way to separate application Ser. No. 09/901,782 filed 9 Jul. 2001, which claim biotinylated from non-biotinylated molecules as described provisional priority to U.S. Provisional Patent Application herein. This system permits the capture of DNA molecules, Ser. No. 60/216,594, filed 7 Jul. 2000, all of which are incor RNA molecules, DNA and RNA-binding proteins, and porated herein by reference. sequence specific transcripts. 0011. The expanding need for higher throughput tech BACKGROUND OF THE INVENTION nologies suggests that the demand for both fluorescently labeled-ATPs and biotinylated-ATPs will increase. Thus, 0002 1. Field of the Invention there is a need in the art for reagents to label both oligonucle 0003. The present invention relates to labeled nucleotides otide and polynucleotides and polypeptide, proteins, (NTPs), to method for making labeled NTPs and to method enzymes, monosaccharides, polysaccharides, or mixtures or for using labeled NTPs such as a method of transferring the combinations thereof with labels having a readily detectable label to a target molecule. property. 0004 More particularly, the present invention relates to gamma (Y) phosphate labeled nucleotides (NTPs), where the DEFINITIONS label includes a detectable tag and an optional linker inter 0012. The term “tag” or “label means an atom or mol posed between the tag and the Y phosphate, to method for ecule that has a detectable property and is capable of being making Y phosphate labeled NTPs and to method for trans attached to a Y phosphate of a nucleotide triphosphate. ferring the Y phosphate and the label to a target molecule 0013 The term “detectable property” means a physical or including an oligonucleotide, a polynucleotide, a polypep chemical property of a tag that is capable of independent tide, a protein, a monosaccharide, a polysaccharide, or mix detection and/or monitoring by an analytical technique after tures or combinations thereof. being attached to a target bio-molecule, i.e., the property is 0005 2. Description of the Related Art capable of being detected in the presence of the system under 0006. Many labeling procedures have been developed analysis. The property can be light emission after excitation, over the years for labeling nucleotide and polypeptide quenching of a known emission sites, electron spin, radio sequences with both radio and non-radio labels. These meth activity (electron emission, positron emission, alpha particle ods are routinely used to aid our understanding of molecular, emission, etc.), nuclear spin, color, absorbance, near JR cellular and intercellular dynamics and interaction. However, absorbance, UV absorbance, far UV absorbance, etc. there are few relatively simple and versatile reagents and 0014. The term “analytical technique' means an analytical methods for attaching non-radio labels to both nucleotide chemical or physical instrument for detecting and/or moni sequence (DNA, RNA, DNA-RNA, etc.), peptide sequences toring the property. Such instruments are based on spectro (polypeptides, proteins, enzymes, macro-assembly, etc.) or scopic analytical methods such as electron spin resonance mixtures or combinations thereof (ribozymes, peptide-nucle spectrometry, nuclear magnetic resonance (NMR) spectrom otide mixed sequences, etc.).
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