25-base DNA strands were studied using a coarse-grained model and Monte Carlo molecular simulation with varied strand lengths. The effect of temperature, strand length, location of complementarity, and surface binding were investigated. Results were analyzed in terms of hydrogen bonding energies and structural properties to understand the duplexes' relative stability. It was found that for shortened complements, the duplex is most stable when the shortened strand binds to the end furthest away from the surface.

Impact of DNA strand length on duplex stability in solution and in a microarray environment via molecular simulation

253rd National Meeting (2017)

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