DNA microarrays are systems consisting of single stranded DNA that is bound to a surface, the probe strand, which hybridizes with its complement that is free to move in solution, the target strand. For this study Monte Carlo molecular simulations were done to look at the effects of target and probe length as well as sequence on hybridization of DNA microarrays for a 25-base strand with a complementary 10-base strand.  Four alternate surface bindings were used – either the long strand at the 3' or 5' end, or the short strand at its 3' or 5' end.  Compared to hybridization with both strands being free to move, duplex destabilization occurred with setups having non-complementary bases on the target directed towards the surface as well as those having non-complementary bases on the probe directed away from the surface.

Effect of unequal strand length on DNA hybridization in a model microarray system via Monte Carlo simulation

249th National Meeting (2015)

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