Surfaces functionalized with ssDNAs can be used to uniquely and reversibly bind complimentary DNAs. Such DNA modified materials are used in nanoscale supramolecular assembly, as optical, electrochemical and piezoelectric biosensors. Recognition and recombination pathways of DNA functionalized system are regulated by ssDNA hybridization. We conducted molecular dynamics simulation studies of DNA strands thiolated on the surface and in the presence of duplex and compared theirdynamics to the dynamics of the DNA strands in solution. We investigated theoptimal ssDNA length, effect of linker type and length to understand the effectof immobilization on subsequent DNA hybridization. Our results indicate that sensitivity and selectivity are directly dependent on the length and sequence of ssDNA strands. Our study helps understanding the science associated with the ssDNA hybridization and provides feedback to the associated experiments.

Molecular dynamics simulations of DNA-based assembly of materials

241st National Meeting (2011)

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