AMBER Archive (2002)

Subject: timescale of deoxyribose ring repuckering

From: Jake Isaacs (rjisaa0_at_uky.edu)
Date: Tue Jan 22 2002 - 10:43:40 CST

What is the current consensus on the timescale of deoxyribose ring
repuckering in double-helical DNA in solution? I've come across some
references that state approximately 10 ns, while others suggest several
north-south transitions per ns. I'm just wondering how many transitions in
an MD simulation would be closest to nature, and how long to conduct an MD
run to approach a statistically relevant ensemble for studying repuckering
in a particular sequence.

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