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O4-alkyl-2'-deoxythymidine cross-linked DNA to probe recognition and repair by O6-alkylguanine DNA alkyltransferases.

Author(s): McManus FP, O'Flaherty DK, Noronha AM, Wilds CJ

Org Biomol Chem. 2012 Sep 21;10(35):7078-90 Authors: McManus FP, O'Flaherty DK, Noronha AM, Wilds CJ

Article GUID: 22850722
Preparation of covalently linked complexes between DNA and O(6)-alkylguanine-DNA alkyltransferase using interstrand cross-linked DNA.

Author(s): McManus FP, Khaira A, Noronha AM, Wilds CJ

Bioconjug Chem. 2013 Feb 20;24(2):224-33 Authors: McManus FP, Khaira A, Noronha AM, Wilds CJ

Article GUID: 23347328
Structural basis of interstrand cross-link repair by O6-alkylguanine DNA alkyltransferase.

Author(s): Denisov AY, McManus FP, O'Flaherty DK, Noronha AM, Wilds CJ

Org Biomol Chem. 2017 Oct 11;15(39):8361-8370 Authors: Denisov AY, McManus FP, O'Flaherty DK, Noronha AM, Wilds CJ

Article GUID: 28937154
Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

Author(s): Copp W, Denisov AY, Xie J, Noronha AM, Liczner C, Safaee N, Wilds CJ, Gehring K

Nucleic Acids Res. 2017 Sep 29;45(17):10321-10331 Authors: Copp W, Denisov AY, Xie J, Noronha AM, Liczner C, Safaee N, Wilds CJ, Gehring K

Article GUID: 28973475
Altering Residue 134 Confers an Increased Substrate Range of Alkylated Nucleosides to the E. coli OGT Protein.

Author(s): Schoonhoven NM, O'Flaherty DK, McManus FP, Sacre L, Noronha AM, Kornblatt MJ, Wilds CJ

Molecules. 2017 Nov 11;22(11): Authors: Schoonhoven NM, O'Flaherty DK, McManus FP, Sacre L, Noronha AM, Kornblatt MJ, Wilds CJ

Article GUID: 29137116
Title:Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.
Authors:Copp W,  Denisov AY,  Xie J,  Noronha AM,  Liczner C,  Safaee N,  Wilds CJ,  Gehring K
Link:https://www.ncbi.nlm.nih.gov/pubmed/28973475?dopt=Abstract
Category:Nucleic Acids Res
PMID:28973475
Dept Affiliation: CHEMBIOCHEM
1 Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.
2 Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada.
3 Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada.

Description:

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

Nucleic Acids Res. 2017 Sep 29;45(17):10321-10331

Authors: Copp W, Denisov AY, Xie J, Noronha AM, Liczner C, Safaee N, Wilds CJ, Gehring K

Abstract

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.

PMID: 28973475 [PubMed - indexed for MEDLINE]