Molecular dynamics simulations were conducted on a system consisting of a
decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a
relatively dry state for the DNA molecule. Simulations were performed at two different
temperatures, 300 K and 450 K. The B-form DNA structure was shown to be stable at
both temperatures. The analysis of hydrogen bonds between trehalose/water and DNA
revealed that trehalose and backbone DNA formed the largest number of hydrogen bonds
and thus constituted the major effect of structural protection for DNA. The number of
hydrogen bonds formed by each OH group of trehalose with the backbone DNA was
compared. Different types of trehalose-DNA interactions were analyzed, with no
prevalent pattern recognized. Diffusion constants for trehalose and water were also
calculated, suggesting a glassy/viscose state of the simulation system. It is believed that
trehalose protects DNA in the dry state through the network of hydrogen bonds built by
the sugars, which reduces the structural fluctuations of DNA and prevents its denaturation.
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/86002 |
| Date | 10 October 2008 |
| Creators | Fu, Xuebing |
| Contributors | Gao, Yiqin |
| Publisher | Texas A&M University |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | Book, Thesis, Electronic Thesis, text |
| Format | electronic, born digital |
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