Messages

1

General discussions (Q&As) / Re: determining helical pitch of curved DNA

« on: December 10, 2013, 02:53:06 pm »

Hi, Xiang-Jun,

thanks very much for the reply and for the helpful hints.
The paper "Two perspectives on the twist of DNA" by Tobias et al. was very useful in understanding the exact definition of twist, writhe and linking number.
In this paper the authors introduced a new property called the "twist of supercoiling", which is different from base-pair step twist, but is connected to the topological invariants, the linking number and the writhing number.
So far I have found only one paper ( http://www.ncbi.nlm.nih.gov/pubmed/21482100 Olson & Zhurkin "Working the kinks out of nucleosomal DNA", Figure 3) which shows this property calculated for real structures, although the authors do not provide and reference to a software package that was used.

I wonder if there are plans to implement such a property for calculation in 3DNA?

Best wishes,
Alexey

2

General discussions (Q&As) / determining helical pitch of curved DNA

« on: December 04, 2013, 06:12:20 pm »

Dear Xiang-Jun,

I would like to ask your advice on I couple of questions.

1) I'm using 3DNA to analyze DNA parameters in nucleosome, both in crystal structures and after MD simulations.
It has been speculated for quite some time, that the DNA in nucleosomes is over twisted (approx. 10 bp per turn instead of 10.5), so I want to show this using 3DNA analysis. An intuitive way to get the value of average helical pitch would be summing the values of twist returned by 3DNA along the DNA and dividing by the number of base pairs. However, I'm not quite sure if this approach is rigorous, and whether one should sum up the values of helical twist of dimer step twist. What do you think?

2) During MD simulations some base pairs might become distorted and they are not found by find_pairs. I can force the calculations on them by manually editing .inp file, however, I assume that the Twist, Roll, Tilt values reported for the base pair steps would be arbitrary.
Will the summation of all twist angles along the DNA helix be meaningful in this case in order to obtain overall twist of the DNA helix?


Thank you in advance,
Alexey