Simulation and modeling of nucleic acid structure, dynamics and interactions

Current Opinion in Structural Biology

Volumn 14, Issue 3, 2004, Pages 360-367

  Cheatham III, Thomas E ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

4 ,6 diamidino 2 phenylindole; DAPI; MD; Molecular dynamics

Indexed keywords

DNA; NANOPARTICLE; NUCLEIC ACID;

BINDING AFFINITY; CIRCULAR DICHROISM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; DNA SEQUENCE; DNA STRUCTURE; DRUG DNA BINDING; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN STABILITY; REVIEW; RNA STRUCTURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; DNA; IONS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHARMACEUTICAL PREPARATIONS; SOLVENTS;

EID: 2942547665     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.05.001     Document Type: Review

References (85)

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13. Spackova N., Cheatham T.E. III, Ryjacek F., Lankas F., van Meervelt L., Hobza P., Sponer J. Molecular dynamics simulations and thermodynamic analysis of DNA-drug complexes. Minor groove binding between 4′, 6-diamidino-2- phenylindole (DAPI) and DNA duplexes in solution. J Am Chem Soc. 125:2003;1759-1769 A rather large set of simulations under varying conditions with different force fields is applied to probe the interaction of the minor-groove-binding drug DAPI with DNA. Although the voluminous presentation of the data is somewhat hard to follow (in both the main paper and the detailed supplementary material), the take-home lesson is that MD simulation can well reproduce these subtle drug-DNA interactions and that MM_PBSA methods, including a finite representation of the explicit solvent, can be used to infer relative binding affinities. The results of the simulations in explicit water with Ewald methods do not appear to be profoundly sensitive to the choice of drug or DNA force field.
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31. •], despite the different restraining method and applied force field.
32. •]).
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