Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies

François, Jean‐Christophe; Saison‐Behmoaras, Tula; Hélène, Claude

doi:10.1093/nar/16.24.11431

Cited by 137 publications

(75 citation statements)

References 26 publications

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“…Homopyrimidine oligonucleotides bind to the major groove of DNA at homopurine-homopyrimidine sequences where they form a triple helix (4)(5)(6). Thymine and protonated cytosine form two hydrogen bonds with A-T and G-C base pairs (bp), respectively.…”

Section: Dnamentioning

confidence: 99%

Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide.

Takasugi

Guendouz

Chassignol

et al. 1991

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

232

165

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On the basis of the structure of DNA-psoralen bis adducts (formed by psoralen with two thymines on opposite strands), a psoralen-oligonucleotide conjugate was designed to photoinduce a cross-link between the two DNA strands at a specific sequence. Psoralen was attached via its C-5 position to a 5'-thiophosphate group of an 11-mer homopyrimidine oligonucleotide. The 11-mer binds to an 11-base-pair homopurinehomopyrimidine sequence of a DNA fragment, where it forms a triple helix. Upon near-UV-irradiation, the two strands of DNA are crosslinked at the TpA step present at the triplex-duplex junction. The reaction is specific for the homopurine'homopyrimidine DNA sequence and requires both oligonucleotide recognition of the DNA major groove and intercalation of psoralen at the triplex-duplex junction. The yield of the photoinduced cross-linking reaction is quite high (>80%). Such psoralen-oligonucleotide conjugates are probes of sequencespecific triple-helix formation and could be used to selectively control gene expression or to induce site-directed mutations.

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Section: Dnamentioning

confidence: 99%

Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide.

Takasugi

Guendouz

Chassignol

et al. 1991

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

232

165

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“…Thus, at each of the two steps, TpG and GpT, present in the third strand a backbone distortion is expected and is associated with an energy penalty. This could explain part of the important decrease in the third strand half-dissociation temperature shown in To analyze more precisely the mode of binding of the 10-base third strands, footprinting experiments were performed at 4°C, using the copper-phenanthroline complex (Cu(OP)2] as an artificial nuclease (21) and a 29-bp fragment as a target. Treatment ofthe 29-bp duplex with Cu(OP)2 in the presence of mercaptopropionic acid led to cleavage reactions along the target strands with an efficiency depending on the local base sequence (Fig.…”

Section: Pair (T-a-t and A-a-t Base Triplets)mentioning

confidence: 99%

Triple-helix formation by oligonucleotides containing the three bases thymine, cytosine, and guanine.

Giovannangéli

Rougée

Garestier

et al. 1992

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

125

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A homopurine-homopyrimidine sequence of human immunodeficiency virus (HIV) proviral DNA was chosen as a target for triple-helix-forming oligonucleotides. An oligonucleotide containing three bases (thymine, cytosine, and guanine) was shown to bind to its target sequence under physiological conditions. This oligonucleotide is bound in a parallel orientation with respect to the homopurine sequence. Thymines recognize A-T base pairs to form TA-T base triplets and guanines recognize a run of G-C base pairs to form G-G-C base triplets. A single 5-methylcytosine was shown to stabilize the triple helix when incorporated in a stretch of thymines; it recognizes a single GC base pair in a run of AT base pairs. These results provide some of the rules required for choosing the more appropriate oligonucleotide sequence to form a triple helix at a homopurine-homopyrimidine sequence of duplex DNA. A psoralen derivative attached to the oligonucleotide containing thymine, 5-methylcytosine, and guanine was shown to photoinduce cross-linking of the two DNA strands at the target sequence in a plasmid containing part of the HIV proviral DNA sequence. Triplex formation and cross-linking were monitored by inhibition of Dra I restriction enzyme cleavage. The present results provide a rational basis for the development of triplex-forming oligonucleotides targeted to specific sequences of the HIV provirus integrated in its host genome.Short oligonucleotides can bind to the major groove of double-stranded DNA at homopurine-homopyrimidine sequences. This was first demonstrated by sequence-specific cleavage with azidoproflavine used to photoinduce crosslinking of the oligonucleotide followed by alkaline cleavage (1) or EDTA-Fe to induce cleavage under reducing conditions (2). Oligonucleotides containing thymine and cytosine bind in a pH-dependent manner with a parallel orientation with respect to the homopurine strand of homopurinehomopyrimidine sequences on double-stranded DNA (3-12). Cytosine methylation was shown to stabilize these triple helices (5, 6) as previously observed on polydeoxynucleotides with alternating sequences (13). Purine-rich oligonucleotides can also bind to homopurine-homopyrimidine sequences (14, 15). The third strand binds in an antiparallel orientation with respect to the homopurine sequence in contrast to homopyrimidine oligonucleotides. This orientation was also found with oligonucleotides containing guanine and thymine or guanine, thymine, and adenine (14). However, energy minimization studies in our laboratory have suggested that third-strand orientation might depend on the number of ApG and GpA steps in the homopurine sequence (16, 17). Here we show that an oligonucleotide containing three bases (thymine, cytosine, and guanine) binds in a parallel orientation with respect to the homopurine sequence of a homopurine-homopyrimidine target of human immunodeficiency virus (HIV) proviral DNA (5'-A4GA4G6A-3' for the purine strand). Binding of this oligonucleotide to its target sequence depends very little on p...

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“…[1][2][3] The specificity of TFO binding is derived from the base triplets formed by either Hoogsteen or reverse Hoogsteen hydrogen bonds formed between the third strand and the purine strand of the duplex. 4 Triplex formation follows a specific binding code imposed by several structural constraints. In the purine motif, a GA or GT-rich TFO binds antiparallel to the purine strand of the duplex through reverse Hoogsteen bonds with the canonical triplets being G.G:C, A.A:T or T.A:T. In the pyrimidine motif, a TC-rich TFO binds in a parallel orientation to the purine strand of the duplex through Hoogsteen bonds, with the canonical triplets being T.A:T and C + .G:C. Due to their sequence specificity, TFOs have been used for targeted genome modifications.…”

Section: Introductionmentioning

confidence: 99%

Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

Rogers

Lloyd

Tiwari

2014

Artificial DNA: PNA & XNA

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Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies

Cited by 137 publications

References 26 publications

Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide.

Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide.

Triple-helix formation by oligonucleotides containing the three bases thymine, cytosine, and guanine.

Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

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