Derivatization of Oligonucleotides Through Abasic Site Formation

Vasseur, Jean‐Jacques; Peoc'h, Didier; Rayner, Bernard; Imbach, Jean‐Louis

doi:10.1080/07328319108046439

Cited by 29 publications

(16 citation statements)

References 22 publications

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“…Interestingly, it has been suggested that the ratio of the anomeric forms may depend upon the identity of the base in the complementary strand ( 8 , 57 ). AP sites have been also generated in oligonucleotides by thermal depurination of either normal ( 63 ) or alkylated purines ( 64 ), but unfortunately there are no reports on their structure. Our results suggest that direct structural comparison between enzymatically and nonenzymatically generated AP sites, in the same sequence context and conditions, will be essential to fully understand the biological consequences of this ubiquitous lesion.…”

Section: Discussionmentioning

confidence: 99%

Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Barbado

Córdoba-Cañero

Ariza

et al. 2018

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

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SignificanceAbasic (apurinic/apyrimidinic, AP) sites in DNA result from spontaneous and repair-mediated base release. They may be processed by AP endonucleases or AP lyases, but the relative roles of both types of enzymes are poorly understood. Our study reveals that the model plant Arabidopsis uses an AP lyase-dependent pathway to repair AP sites generated by spontaneous loss of N7-methylguanine (N7-meG), a major lesion arising from DNA methylation damage. We further show that the main Arabidopsis AP endonuclease is active on AP sites generated by enzymatic excision of N7-meG, but not on those arising from N7-meG loss. Our findings identify an important role for AP lyase activity in plants and challenge the assumption that spontaneous and repair-generated AP sites have identical biochemical properties.

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Section: Discussionmentioning

confidence: 99%

Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Barbado

Córdoba-Cañero

Ariza

et al. 2018

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

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“…The authors introduced the deoxyuridine residue at selected positions of oligomers by automated solid phase synthesis and generated the abasic site by treatment of the resulting oligonucleotide with uracil DNA-glycosylase. The greater lability of purine residues in acidic conditions has been used in early studies by Vasseur et al 11,12 to prepare oligodeoxypyrimidines containing abasic sites by hydrolysis of N-benzoyl-adenosine residues. 11 Other nucleotide analogues, such as 2-pyrimidinone-deoxynucleotide, 13 are transformed into AP-sites under mild acidic conditions (pH 3, room temperature).…”

Section: Abasic Sites Generation-synthesis Of Abasic Dnamentioning

confidence: 99%

Abasic DNA structure, reactivity, and recognition

1999

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“…The ion exchange HPLC experiments (Table 1) demonstrated that the retention times ofthe circular (9) and looped (14-17) oligonucleotides were longer than those of their bis-disulfide precursors (7, 18, 20, 22 and 24). Dithiols (8,19,21,23 and 25) were retained more efficiently than their bis-disulfide precursors, but less efficiently than the circular or looped oligonucleotides. This observation was utilized in monitoring the cross-linking reactions.…”

Section: Hplcmentioning

confidence: 99%

“…The antigene strategy is in turn based on inhibition of transcription or replication of genes due to the interaction of synthetic oligonucleotides with DNA (3). Recently, bimolecular triple helices have found use in a new strategy for DNA and RNA recognition (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). This approach is based on selective and strong complexing of a purine-rich sequence of the target nucleic acid with two pyrimidine-rich fragments of the complementary oligonucleotide.…”

Section: Introductionmentioning

confidence: 99%

Looped oligonucleotides form stable hybrid complexes with a single-stranded DNA

Azhayeva¹,

Azhayev²,

Guzaev³

et al. 1995

Nucl Acids Res

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Several new branched (1, 2), circular (9) and looped oligonucleotides (14-17) were synthesized. 3'-Deoxypsicothymidine was employed to create the site of branching when required. The circular and looped structures were obtained by oxidative disulfide bond formation between mercaptoalkyl tether groups. All the oligonucleotides prepared contained two T11 sequences, and the branched and looped oligomers an additional alternating CT sequence. The melting experiments revealed that the branched oligonucleotides form relatively weak hybrid (double/triple helix) complexes with the single-stranded oligodeoxyribonucleotide, showing a considerable destabilizing effect produced by the structure at the point of branching. The data obtained with looped oligonucleotides demonstrated considerable stabilization of the hybrid (double/triple helix) complexes with the complement. The data reported may be useful in attempting to design new antisense or antigene oligonucleotides capable of forming selective and stable bimolecular hybrid complexes with nucleic acids.

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Derivatization of Oligonucleotides Through Abasic Site Formation

Cited by 29 publications

References 22 publications

Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Abasic DNA structure, reactivity, and recognition

Looped oligonucleotides form stable hybrid complexes with a single-stranded DNA

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