(214y) Mechanical Deformation of dsDNA: Molecular Modeling Approach

                                       Mechanical Deformation of dsDNA: Molecular Modeling Approach

Hyea Hennim Hwang, Byeong Jae Chun and Seung Soon Jang

School of Materials Science and Engineering, Georgia Institute of Technology,

771 Ferst Drive, Atlanta, GA 30332-0245

Harold D. Kim

School of Physics, Georgia Institute of Technology,

837 State Street, Atlanta, GA 30332-0430

Studying sequence-dependent DNA dynamics is crucial for understanding the relationship between DNA sequence and genome function, which is one of the holy grails of biology. For this purpose, molecular dynamics (MD) simulation can provide detailed information on structural changes of DNA at resolution not yet accessible to current experimental techniques. In this study, we use MD simulation to investigate the structural changes that double-stranded DNA (dsDNA) undergoes during mechanical deformation and measure how stress is distributed in this process. In our simulations, a 9 base pair B-DNA duplex is tethered at two H-terminated Si (111) surfaces through spacers, and is extended by pulling these surfaces apart at a constant rate.  The change of stress required for extension is monitored as a function of strain. During the extension, the structural change is analyzed in terms of the hydrogen bonding geometry in each base pair, the torsion angles along backbone, diameter of double helical structure. Transition state from double helix to a novel ladder structure is also analyzed, in which base pairs of one strand are stacked on those of the other strand.  By designing the base sequence for simulations,  the sequence-dependency of mechanical deformation is elucidated.