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Molecular Codes - Biomatics.org

Molecular Codes

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Molecules, especially long chain molecules such as DNA and proteins have many possible ways of coding information and algorithms. One possible such modality may lie in the rates at which successive covalent bonds rotate about their respective carbon atoms. The Histone tails may be one example of such functioning. Heretofore so-called "unstructured" proteins may function in this way. One way to analyze such molecules is to fix them at one end and study the pattern made by the free end as the covalent bonds rotate. 

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We continue to study a small but ubiquitous RNA structural motif known as the GNRA tetraloop. This structure plays a role in the formation of larger RNA’s and is also of great interest due to its statistical overabundance in RNA structure. Our study demonstrates the highly flexible and dynamic properties of this structure, and also highlights the ability of this sequence to take on a number of non-native configurations in order to interact with adjacent RNA strands, suggesting that conformational entropy acts to stabilize this loop when not in its native conformation.

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

http://folding.stanford.edu/English/Papers

 

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