Simulations of DNA distortions by a CIS, SYN cyclobutane thymine dimer

Conference · Wed Dec 31 04:00:00 EST 1997

OSTI ID:559992

Miller, J H; Cooney, M G ^[1]; Miaskiewicz, K ^[2]

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1. Pacific Northwest National Lab., Richland, WA (United States)
2. DASGroup, Inc., Johnstown, PA (United States); and others

Molecular dynamics simulations were preformed on the DNA dodecamers CGCGAATTCGCG and GCACGAATTAAG, where TT denotes a thymine dimer. The constant temperature and pressure algorithm of AMBER 4.1 was used with explicit water and counterions, periodic boundary conditions, and electrostatic interactions evaluated by the particle-mesh Ewald method. Results were analyzed by the CURVES algorithm and its implementation in DIALS and WINDOWS. Calculated distortions of DNA structure were qualitatively and quantitatively similar for the two sequences. Despite the enhanced flexibility of the native TpA dinucleotide step, major deviations from the B-DNA values of helicoidal parameters were found only at the ApT and TpT dinucleotide steps in both sequences. Hence, we conclude that the pattern of structural perturbations responsible for recognition of thymine dimers by repair enzymes is not sensitive to their sequence context.

• OSTI ID: 559992
• Report Number(s): CONF-970443--
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
BOUNDARY CONDITIONS
DIMERS
DNA
DNA REPAIR
ENZYMES
SIMULATION