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A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

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 In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA–DNA attractions.

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Received: 30 November 2000 / Accepted: 7 February 2001 / Published online: 22 May 2001

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Wong, KY., Montgomery Pettitt, B. A study of DNA tethered to a surface by an all-atom molecular dynamics simulation. Theor Chem Acc 106, 233–235 (2001). https://doi.org/10.1007/s002140100269

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  • DOI: https://doi.org/10.1007/s002140100269

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