Keyword search (3,448 papers available)


Recent Advances of DNA Tetrahedra for Therapeutic Delivery and Biosensing.

Author(s): Copp W, Pontarelli A, Wilds CJ

The chemical and self-assembly properties of nucleic acids make them ideal for the construction of discrete structures and stimuli-responsive devices for a diverse array of applications. Amongst the various three-dimensional assemblies, DNA tetrahedra are o...

Article GUID: 33506614
O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron.

Author(s): Copp W, Wilds CJ

Chemistry. 2020 Jun 16;: Authors: Copp W, Wilds CJ

Article GUID: 32543755
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
Backbone Flexibility Influences Nucleotide Incorporation by Human Translesion DNA Polymerase η opposite Intrastrand Cross-Linked DNA.

Author(s): O'Flaherty DK, Guengerich FP, Egli M, Wilds CJ

Biochemistry. 2015 Dec 29;54(51):7449-56 Authors: O'Flaherty DK, Guengerich FP, Egli M, Wilds CJ

Article GUID: 26624500
O(6)-Alkylguanine DNA Alkyltransferase Repair Activity Towards Intrastrand Cross-Linked DNA is Influenced by the Internucleotide Linkage.

Author(s): O'Flaherty DK, Wilds CJ

Chem Asian J. 2016 Feb 18;11(4):576-83 Authors: O'Flaherty DK, Wilds CJ

Article GUID: 26692563
Stabilization of i-motif structures by 2'-β-fluorination of DNA.

Author(s): Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ

Nucleic Acids Res. 2016 06 20;44(11):4998-5009 Authors: Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ

Article GUID: 27166371
Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes.

Author(s): Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT

Nucleic Acids Res. 2016 07 08;44(12):5849-60 Authors: Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT

Article GUID: 27220465
Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.

Author(s): O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ

Chem Sci. 2016 Aug 01;7(8):4896-4904 Authors: O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ

Article GUID: 27574558
Preparation of Intrastrand {G}O(6) -Alkylene-O(6) {G} Cross-Linked Oligonucleotides.

Author(s): O'Flaherty DK, Wilds CJ

Curr Protoc Nucleic Acid Chem. 2016 09 01;66:5.17.1-5.17.24 Authors: O'Flaherty DK, Wilds CJ

Article GUID: 27584704
O6-2'-Deoxyguanosine-butylene-O6-2'-deoxyguanosine DNA Interstrand Cross-Links Are Replication-Blocking and Mutagenic DNA Lesions.

Author(s): Xu W, Kool D, O'Flaherty DK, Keating AM, Sacre L, Egli M, Noronha A, Wilds CJ, Zhao L

Chem Res Toxicol. 2016 11 21;29(11):1872-1882 Authors: Xu W, Kool D, O'Flaherty DK, Keating AM, Sacre L, Egli M, Noronha A, Wilds CJ, Zhao L

Article GUID: 27768841
Site-specific covalent capture of human O6-alkylguanine-DNA-alkyltransferase using single-stranded intrastrand cross-linked DNA.

Author(s): O'Flaherty DK, Wilds CJ

Org Biomol Chem. 2016 Dec 20;15(1):189-196 Authors: O'Flaherty DK, Wilds CJ

Article GUID: 27886318
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
AGT Activity Towards Intrastrand Crosslinked DNA is Modulated by the Alkylene Linker.

Author(s): O'Flaherty DK, Wilds CJ

Chembiochem. 2017 12 05;18(23):2351-2357 Authors: O'Flaherty DK, Wilds CJ

Article GUID: 28980757
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
Covalent capture of OGT's active site using engineered human-E. coli chimera and intrastrand DNA cross-links.

Author(s): Copp W, O'Flaherty DK, Wilds CJ

Org Biomol Chem. 2018 11 28;16(46):9053-9058 Authors: Copp W, O'Flaherty DK, Wilds CJ

Article GUID: 30430154
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]