Infrared demonstration of two- and three-strand helix formation between poly C and guanosine mononucleotides and oligonucleotides

Howard, Frank B.; Frazier, Joe; Lipsett, Marie N.; Miles, H. Todd

doi:10.1016/0006-291x(64)90306-7

Cited by 121 publications

(55 citation statements)

References 6 publications

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“…The sequence-specific recognition of DNA duplexes by a third strand (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12), has implications in gene-regulation and site specific cleavage of genomic DNA (13)(14)(15). There have been several NMR studies on the structural characterization of pyrimidine(Y).purine(R):pyrimidine(Y) DNA triplexes (throughout this paper, Watson and Crick base pairs are represented as R:Y, Hoogsteen as YR and mismatch as R-Y).…”

Section: Introductionmentioning

confidence: 99%

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

Bhaumik¹,

Chary²,

Govil³

et al. 1995

Nucl Acids Res

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Homo-purine (d-TGAGGAAAGAAGGT) and homopyrimidine (d-CTCCT TI CTTCC) oligomers have been designed such that they are complementary in parallel orientation. When mixed in a 1:1 molar ratio, the system adopts an antiparallel duplex at neutral pH with three mismatched base pairs. On lowering the pH below 5.5, a new complex is formed. The NMR results show the coexistence of a intermolecular pyrimidine.purine:pyrimidine DNA triplex and a single stranded oligopurine at this pH.

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Section: Introductionmentioning

confidence: 99%

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

Bhaumik¹,

Chary²,

Govil³

et al. 1995

Nucl Acids Res

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“…The ODNs bind in the major groove of DNA such that the pyrimidine ODN is parallel to the purine strand of the duplex. Because of the requirement for cytosine to be protonated, ODNs containing C form a triple helix in a pH-dependent manner since the pKa of cytosine is 4.5 (7)(8)(9). Evidence for another structural class of triple helix was described by Cooney et al (10), who showed that G-rich ODNs can specifically bind to polypurine tracts of duplex DNA wherein G recognizes G-C base pairs and A recognizes A-T base pairs.…”

mentioning

confidence: 99%

Triple helix formation inhibits transcription elongation in vitro.

Young

Krawczyk

Matteucci

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

186

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We have identified a 15-nucleotide site within a G-free transcription cassette that forms triple helix with sequence-specific oligodeoxyribonucleotides. When oligodeoxynucleotides were added to template DNA prior to in vitro transcription, a significant fraction of transcripts were truncated at a site corresponding to the region of triple helix formation. Kinetic analysis of the transcription products demonstrated that these truncated transcripts could be elongated to full length upon prolonged incubation. When an alkylating base was incorporated into the oligodeoxynucleotide to form covalent triple helix, most of the transcripts remained truncated. We conclude that triple helix formation can stall or, in the case of covalent crosslinking, can block RNA polymerase II and thus may provide a method for the specific inhibition of gene expression.

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“…Guanosine mononucleotide binds to poly(C) by forming a Watson-Crick base pair (29). The orientation of the sugar-phosphate component of the monomer relative to the template is determined by the handedness of the ribose sugar (D VS. L) and the rotational conformation about the glycosidic bond (syn vs. anti).…”

mentioning

confidence: 99%

The case for an ancestral genetic system involving simple analogues of the nucleotides.

Joyce¹,

Schwartz²,

Miller³

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

358

181

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The idea that the first living systems on earth were based on self-replicating RNA molecules has recently become popular as a result of the discovery of ribozymes. However, there are several major problems associated with the prebiotic synthesis of ribonucleotides. In addition, there is the newly recognized problem of enantiomeric cross-inhibition, whereby template-directed polymerization involving one enantiomer of RNA is inhibited strongly by the presence of the other enantiomer. Here we propose that RNA was preceded in the evolution of life by a polymer constructed from flexible, acyclic, probably prochiral nucleotide analogues that were synthesized readily on the primitive earth. Several potentially prebiotic nucleotide analogues are considered in this context, and some of the consequences of this proposal are discussed.

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Infrared demonstration of two- and three-strand helix formation between poly C and guanosine mononucleotides and oligonucleotides

Cited by 121 publications

References 6 publications

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

Triple helix formation inhibits transcription elongation in vitro.

The case for an ancestral genetic system involving simple analogues of the nucleotides.

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