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Nucleic Acid Analogue Induced Transcription of Double Stranded DNA

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Nucleic Acid Analogue Induced Transcription of Double Stranded DNA Downloaded from orbit.dtu.dk on: Sep 26, 2021 Nucleic Acid Analogue Induced Transcription of Double Stranded DNA Berg, Rolf Henrik; Buchardt, Ole; Engholm, Michael; Nielsen, Peter E. Publication date: 1998 Link back to DTU Orbit Citation (APA): Berg, R. H., Buchardt, O., Engholm, M., & Nielsen, P. E. (1998). Nucleic Acid Analogue Induced Transcription of Double Stranded DNA. (Patent No. US5837459). General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. US005837459A Ulllted States Patent [19] [11] Patent Number: 5,837,459 Berg et al. [45] Date of Patent: Nov. 17, 1998 [54] NUCLEIC ACID ANALOGUE INDUCED [56] References Cited DNTRA AN SCRIPTIO N OF DOUBLE STRA N DED PUBLICATIONS _ _ Daube, et al. 1992, Science, vol. 258 pp. 1320—1324. [75] Inventors: Rolf Hennk Berg’ Fredencksberg’ Nielsen, et al. 1991, Science, vol. 254, pp. 1497—1500. Denmark; Ole Buchardt, deceased, late of Yaerlose, Denmark, by Dorte Primary Examiner—David GuZo Buchardt, heir; Michael Egholm, Attorney, A gent, 0r Firm—Nikaido Marmelstein Murray & Lexington, Mass; Peter Eigil Nielsen, Oram LLP Kokkedal, Denmark [57] ABSTRACT [73] Assignee: Boehringer Mannheim GmbH, RNA is transcribed from a double stranded DNA template Mannheim, Germany by forming a complex by hybridizing to the template at a desired transcription initiation site one or more oligonucleic [21] APP1~NO-:653’605 acid analogues of the PNA type capable of forming a [22] Filed. May 24 1996 transcription initiation site With the DNA and exposing the ’ complex to the action of a DNA dependant RNA polymerase [30] Foreign Application Priority Data in the presence of nucleoside triphosphates. Equal length . transcripts may be obtained by placing a block to transcrip Nov. 25, 1993 [GB] United Kingdom ................. .. 9324245 tion downstream from the initiation Site or by Cutting the [51] Int. Cl.6 ............................. .. C12Q 1/68; C12P 19/34 template at such a selected location. The initiation site is [52] US. Cl. .......................... .. 435/6; 435/911; 435/912; formed by displacement of one strand of the DNA locally by 435/9121 the PNA hybridization. [58] Field of Search ......................... .. 530/300; 536/18.7, 536/243; 435/9121, 91.1, 91.2, 6 59 Claims, 6 Drawing Sheets U S Patent Nov. 17,1998 Sheet 1 of6 5,837,459 Mum U.S. Patent Nov. 17,1998 Sheet 2 of6 5,837,459 Fig. 2 19C 19A T96 PIIA - + - + - + a I ’ U "" a Background ‘ ‘- ‘I 4 . “ ‘'“' RNA transcripts E. cali RNA polymerase Run-aft transcripts from PIA loops containing T. B, C and A. U.S. Patent Nov. 17,1998 Sheet 3 of6 5,837,459 U.S. Patent Nov. 17,1998 Sheet 4 of6 5,837,459 Fig. A A RNA 217-. “vs Al. 5| - '1 3| 3' 5| ——————I'-21[1 RNA B RNA Z33“ ——Ammn 5| - L5A 3| 3' 5| 2Z5 RNA E 2L9< RNA 1L5--_-______ [1V5 AQBTQCTQC 5' - ‘q 3' 3| - 5| >235 RNA U.S. Patent Nov. 17,1998 Sheet 5 of6 5,837,459 U.S. Patent Nov. 17,1998 Sheet 6 of6 5,837,459 Fig . 6 5| ___‘ ,_ 3' RNA 31 S3 S2 UNA-aligonuclealide lRNA dependent - DNA polymerase 5: : 3" DNA 3 S3 5 DNA ‘ RNA polymerase RNA :2’ PM Fig.7 5' W 3' DNADNA—aligan,ucleatide rev. lranscriptase or. DNA dependent - DNA polymerase ————v— denature _ anneal Prlmer ;———————- * UNA dependent -l]NA polymerase 51 ,__-l 3| 3l-—"——-'—-‘‘ 5' RNA polymerase :3 PM RNA 5,837,459 1 2 NUCLEIC ACID ANALOGUE INDUCED tion of a DNA primer of the correct sequence doWnstream TRANSCRIPTION OF DOUBLE STRANDED from the T7 promotor sequence. It is further dependent on DNA obtaining the nucleic acid sequense of interest in the form of RNA. CROSS REFERENCE TO RELATED According to the present invention hoWever, a nucleic APPLICATION acid sequence of interest obtained in the form of double This application is a continuation-in-part of International stranded DNA can be ampli?ed as multiple single stranded Application PCT/EP94/03858, ?led Nov. 22, 1994, and RNA copies by synthesising a primer or multiple primer designating the US. sequences of the nucleic acid analogue, Which Will generally The present invention relates to the use of analogues of be much more straightforward than the prior art methods. naturally occurring nucleic acids to produce sites for the in The RNA transcripts produced can be converted to DNA if vitro initiation of transcription of double stranded DNA, to desired. the production of RNA transcripts thereby, the ampli?cation Accordingly, the present invention provides a method of and/or detection of such transcripts and in vitro diagnostics transcribing RNA from a double stranded DNA template techniques based on the above. 15 comprising forming a complex by hybridising to said tem Analogues of nucleic acids having a peptide or similar plate at a desired transcription initiation site one or more backbone bearing pendant ligands such as nucleic acid bases oligo-nucleic acid analogues capable of forming a transcrip described in WO 92/20703 (PNA’s) have been shoWn to tion initiation site With said DNA and exposing said complex have a number of unusual properties. These include the to the action of a DNA dependent RNA polymerase in the ability to form complexes With double stranded DNA in presence of nucleoside triphosphates. Which tWo strands of PNA complementary in sequence to Optionally, a pair of said oligo-nucleic acid analogues are one of the DNA strands hybridise to the DNA displacing the hybridised to said DNA at spaced locations thereon, on the other DNA strand. A high level of sequence speci?city has same or different strands thereof been shoWn. 25 Preferably, said pair of oligo-nucleic acids are spaced by Transcription of DNA to form a strand of RNA of from 0 to 10, more preferably 0 to 5 base pairs of said DNA. corresponding sequence is initiated in nature by the Preferably also, the or each said oligo-nucleic acid ana sequence speci?c recognition of a promotor region of the logue has a length of from 5 to 60 nucleic acid analogue double stranded DNA either by RNA polymerase or by units. auxiliary transcription factors. Subsequently, a transcription Optionally, a block to transcription is placed at a location initiation open complex is formed in Which about 12 base doWnstream from said desired initiation site so as to produce pairs of the DNA helix is melted so as to expose the bases equal length transcripts in said transcription. A suitable Way of the template strand for base pairing With the RNA strand of producing a said block is by hybridising to said DNA an being synthesised. It has been shoWn that E. coli and phage oligo-nucleic acid analogue capable of blocking transcrip T7 RNA polymerase can utilise synthetic “RNA/DNA 35 tion. OtherWise, individual transcription events may termi bubble duplex” complexes containing an RNA/DNA duplex nate randomly doWnstreams from the initiation site leading and a single stranded DNA D-loop for transcription initia to long transcription products of varying length. tion purposes. The length of the transcripts can also be controlled by We have noW discovered that initiation can similarly be cutting the DNA template With a restriction enZyme at a initiated from a strand displacement complex formed speci?c doWnstream location prior to transcription. betWeen PNA and double stranded DNA. This presents the prospect of having a ready and simple Way of preparing The nucleic acid analogue capable of forming a transcrip single stranded transcripts from a double stranded template. tion initiation site is preferably a compound that has nucleo bases attached to an aminoethylglycine backbone or other Generally, techniques for identifying DNA sequences like backbone including polyamides, polythioanides, depend upon having the DNA in single stranded form. Once 45 polysul?namides and polysulfonamides, Which compounds single stranded, the DNA can be hybridised to a probe of We call peptide nucleic acids or PNA. Compounds of this complementary sequence and such hybridisation can be kind surprisingly bind strongly and sequence selectively to detected in various Ways. Transcription of RNA from a both RNA and DNA. double stranded template DNA presents an alternative form of method for obtaining a single stranded product for The synthesis of this type of compound is fully described detection and unlike processes of denaturation of the origi in WO 92/20703. nal DNA, it avoids the presence of corresponding amounts The recognition by PNA of RNA, ssDNA or dsDNA can of the complementary single stranded product Which can take place in sequences at least 5 bases long. A more compete in the detection process. preferred recognition sequence length is 5—60 base pairs Furthermore, the production of an RNA transcript opens 55 long. Sequences betWeen 10 and 20 bases are of particular the Way for ampli?cation of the original DNA sequence interest since this is the range Within Which unique DNA Without the use of the polymerase chain reaction and Without sequences of prokaryotes and eukaryotes are found.
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