3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: kailsen on March 01, 2013, 11:03:41 pm

Title: DNA/ RNA fibre model values
Post by: kailsen on March 01, 2013, 11:03:41 pm: Dear All,
I would like to known why in fibre models the values of tilt and shift has to be close to zero. i recently built a RNA model from a webserver and it had tilt value of 0.5 and shift value of 1.0. then later i was pointed out that the structure was wrong. I confirmed ten by using w3dna for all adna, bdna and arna that the tilt & shift value is close to zero.
Title: Re: DNA/ RNA fibre model values
Post by: xiangjun on March 02, 2013, 12:01:34 pm: Quote
I would like to known why in fibre models the values of tilt and shift has to be close to zero

The fiber models from 3DNA are based on experimental data, collected from various sources (for details, type "fiber -m"). You observed that in those structures, the values of tilt and shift are close to zero. Note that the fiber models are simplified, averaged, and regular structures. Compared to roll and slide, tilt and shift are normally not as significant in defining DNA or RNA duplex structures. For example, to a first approximation, A- and B-DNA are distinguished by slide and roll, as shown in Figure 4 of the 3DNA NAR03 paper (http://nar.oxfordjournals.org/content/31/17/5108.full).

(http://nar.oxfordjournals.org/content/31/17/5108/F4.large.jpg)

To get a better understanding of DNA structures, see Calladine's book titled "Understanding DNA: The Molecule and How it Works (http://www.amazon.com/Understanding-DNA-Third-Edition-Molecule/dp/0121550893)".

HTH,

Xiang-Jun
Title: Re: DNA/ RNA fibre model values
Post by: kailsen on March 02, 2013, 09:51:30 pm: Thank You so much for the prompt reply