I'm working on a project on investigating the sequence dependent DNA
structure, namely trying to identify the origins of base stacking
interactions. So far, i have evidence that carbonyl oxygen (O16) of the
contact group like to 'sit' on top on central group's carbonyl carbon (C4).
This donor-acceptor non-bonded contact is reinforced by an additional set of
non-bonded interaction, the nitrogen (N3) interacting with carbonyl carbon
(C13). I performed a database search thorugh the Cambridge Strucutral Database
(CSD) and also used novel software - Isostar and Isogen to calculate the
distribution the the contact group on central group.
I hope that someone outthere will have any ideas or currrently working on this
field and want to chat about it.
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