Backbone dynamics of DNA containing 8-oxoguanine: Importance for substrate recognition by base excision repair glycosylases

Mutation Research - DNA Repair

Volumn 487, Issue 3-4, 2001, Pages 93-108

  Dodson, M L ^a   Lloyd, R Stephen ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

AMBER; Glycosylase; Nucleotide flipping; Oxidative DNA damage

Indexed keywords

8 HYDROXYGUANINE; CATION; CYTOSINE; DNA BASE; DNA GLYCOSYLTRANSFERASE; METHYLTRANSFERASE; NUCLEOTIDE;

ARTICLE; BASE PAIRING; CATALYSIS; COMPUTER SIMULATION; CONTROLLED STUDY; DNA CONTENT; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; ENZYME MODIFICATION; ENZYME SUBSTRATE; EXCISION REPAIR; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BINDING SITES; COMPUTER SIMULATION; DNA; DNA DAMAGE; DNA GLYCOSYLASES; DNA REPAIR; GUANINE; MODELS, CHEMICAL; N-GLYCOSYL HYDROLASES; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 0035915403     PISSN: 09218777     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0921-8777(01)00109-4     Document Type: Article

References (33)

1. Initiation of base excision repair: Glycosylase mechanisms and structures
2. DNA repair mechanisms for the recognition and removal of damaged DNA bases
3. Base excision repair family portrait: Integrating the structure and chemistry of an entire DNA repair pathway
4. M.HhaI binds tightly to substrates containing mismatches at the target base
5. Dynamic modes of the flipped-out cytosine during M.HaI methyltransferase-DNA interactions in solution
6. Measurement of the absolute temporal coupling between DNA binding and base flipping
7. DNA totally flipped-out by methylase
8. The crystal structure of HaeIII methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing
9. A nucleotide-flipping mechanism from the structure of human uracil DNA glycosylase bound to DNA
10. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex
11. Base excision repair family portrait: Integrating the structure and chemistry of an entire DNA repair pathway
12. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
13. Defining the structure of irregular nucleic acids: Conventions and principles
14. A quantitative description of the conformation of biological macromolecules
15. Conformational and helicoidal analysis of 30ps of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows
16. Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme
17. MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily
18. Essential dynamics of proteins
19. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
20. A system for induction of oblique decision trees
21. Catalytic mechanism and DNA substrate recognition of Escherichia coli MutY protein
22. Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis
23. Are there non-trivial dynamic cross-correlations in proteins?
24. Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8
25. The MIDAS display system
26. A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model
27. A second generation force field for the simulation of proteins and nucleic acids
28. Modeling unusual nucleic acid structures