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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.
- D. Beveridge, G. Barreiro, +14 authors M. A. Young
- Medicine, Chemistry
- Biophysical journal
- 1 December 2004
We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique… Expand
Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine.
- E. Rachofsky, E. Seibert, J. Stivers, R. Osman, J. B. Ross
- Chemistry, Medicine
- 3 January 2001
Abasic sites are highly mutagenic lesions in DNA that arise as intermediates in the excision repair of modified bases. These sites are generated by the action of damage-specific DNA glycosylases and… Expand
Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase.
Uracil DNA glycosylase (UDG) is a base excision repair enzyme that specifically recognizes and removes uracil from double- or single-stranded DNA. The efficiency of the enzyme depends on the DNA… Expand
Contribution of opening and bending dynamics to specific recognition of DNA damage.
Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs.… Expand
pH-Dependent Spectroscopy and Electronic Structure of the Guanine Analogue 6,8-Dimethylisoxanthopterin †
Fluorescent nucleic acid analogues are valuable tools for studying DNA dynamics, protein−DNA interactions and nucleotide-dependent enzyme activities. The recent development of guanine analogues based… Expand
[Os(bpy)2(CO)(enIA)][OTf]2: a novel sulfhydryl-specific metal-ligand complex.
The synthesis and physical-chemical characterization of the metal-ligand complex [Os(bpy)2(CO)(enIA)][OTf]2 (where enIA = ethylenediamine iodoacetamide) with a sulfhydryl-specific functional group is… Expand
Quantum mechanical investigation of the electronic structure and spectral properties of 6,8-dimethylisoxanthopterin
6-Methylisoxanthopterin (6-MI) is a fluorescent guanine analog that is suitable for studying deoxyribonucleic acid (DNA) structure and dynamics. To aid in the interpretation of spectroscopic data, we… Expand