The effect of unequal strand length on short DNA duplex hybridization in a model microarray system: A Monte Carlo simulation study

[Display omitted] •Molecular simulation of short DNA duplexes with dangling ends carried out.•There is little impact of dangling end on solution hybridization.•Attachment to a surface can strengthen or weaken their hybridization.•The duplex structure can be altered by surface binding and dangling en...

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Bibliographic Details
Published in:Chemical physics letters 2015-08, Vol.634, p.230-235
Main Authors: Cooper, Connor J., Stubbs, John M.
Format: Article
Language:English
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Summary:[Display omitted] •Molecular simulation of short DNA duplexes with dangling ends carried out.•There is little impact of dangling end on solution hybridization.•Attachment to a surface can strengthen or weaken their hybridization.•The duplex structure can be altered by surface binding and dangling ends.•Small targets have generally weaker interactions compared to longer ones. Monte Carlo molecular simulations of DNA decamer–hexamer strands were carried out over a range of temperatures, both free in solution and bound to a surface in several possible fashions, to investigate the effect of dangling end nucleotides on hybridization. For comparison, analogous hexamer duplexes were also studied in solution. Duplex stability was analyzed in terms of energetic, hydrogen bonding, and structural properties. Of the systems studied, shorter solution sequences interacting with longer surface-bound sequences generally had weaker interactions than the opposite.
ISSN:0009-2614
1873-4448
DOI:10.1016/j.cplett.2015.06.024