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:Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes.
Authors:Carter AR,  Seaberg MH,  Fan HF,  Sun G,  Wilds CJ,  Li HW,  Perkins TT
Link:https://www.ncbi.nlm.nih.gov/pubmed/27220465?dopt=Abstract
Category:Nucleic Acids Res
PMID:27220465
Dept Affiliation: CHEMBIOCHEM
1 Department of Physics, Amherst College, Amherst, MA 01002, USA.
2 Department of Physics, University of Colorado, Boulder, CO 80309, USA JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA.
3 Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B1R6, Canada.
4 Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.
5 Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B1R6, Canada.
6 JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA tperkins@jila.colorado.edu.

Description:

Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes.

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

Abstract

RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2-4 µM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (~4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD-DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex. Five observations support this interpretation. First, these dynamics were present in the absence of ATP. Second, the onset of the dynamics was coupled to RecBCD entering into an unwinding-competent state that required a sufficiently long 5' strand to engage the RecD helicase. Third, the dynamics were modulated by the GC-content of the dsDNA. Fourth, the dynamics were suppressed by an engineered interstrand cross-link in the dsDNA that prevented unwinding. Finally, these dynamics were suppressed by binding of a specific non-hydrolyzable ATP analog. Collectively, these observations show that during unwinding, RecBCD binds to DNA in a dynamic mode that is modulated by the nucleotide state of the ATP-binding pocket.

PMID: 27220465 [PubMed - indexed for MEDLINE]