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Author Topic: minor and major grooves  (Read 7255 times)

Offline maryatx3dna

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minor and major grooves
« on: August 17, 2016, 03:10:53 am »
Sir,

i have been using 3DNA for helical parameter calculations.
I have attached 3DNA o/p of two RNA duplexes and a Nucleic acid research paper providing the minor and major grooves of these duplexes (calculated using curves) and standard values of RNA (minor groove 11.0 and major groove 2.7 angstroms) . I would like know your opinion in this matter



standard values are more comparable to curves values.
I need to use 3DNA only as i have modified nucleobased  duplex  and it works with 3DNA.
But i am facing problems when i have to compare with standard values and crystal structures (like 1RNA, !SDR etc)

hoping you valuable suggestions

thanking you

mary

Offline xiangjun

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Re: minor and major grooves
« Reply #1 on: August 17, 2016, 09:55:10 am »
Hi Mary,

It seems that one component of your post is missing (before the line "standard values are more ...").

The comparison of DNA groove widths calculated from 3DNA with those from Curves (or Curves+) is sort of complicated. As noted in the output,  the 3DNA minor/major-groove widths are calculated following the algorithm given in the appendix of the El Hassan and Calladine 1998 JMB paper:

Quote
M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

It uses simple P-P distance measures and does not include groove depths. On the other hand, the Curves (or Curves+) definition is more sophisticated and complete, and gives groove widths and depths. The referred 1999 Tanaka et al. NAR paper used Curves. You may already know that Curves has been replaced by Curves+ (as of 2009).

Whatever program you use, it is important to be consistent for comparisons. You may want to use the same (version) program to analyze all the structures you are interested in. While some (numerical) details are likely to differ between the different programs, the general pattern should be (more or less) consistent.

Xiang-Jun
« Last Edit: August 17, 2016, 01:44:11 pm by xiangjun »

Offline maryatx3dna

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Re: minor and major grooves
« Reply #2 on: August 17, 2016, 01:13:24 pm »
sir,

the component missing was the same nar.jpg attached.

i need to use 3dna only.
but i couldnt compare with the standard A-RNA major groove width which is around 2 angstrom. when standard structures are analyzed with 3dna its around 6 angstroms.

so i dont understand what to do.

also sir i should use P-P refined value. isnt?

thanking you

mary


Offline xiangjun

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Re: minor and major grooves
« Reply #3 on: August 17, 2016, 01:29:25 pm »
Hi mary,

If you want to stay with 3DNA, please also cite the original El Hassan & Calladine reference on the definition of groove widths. Yes, the "refined" P-P distance should be used -- compared to the "raw" P-P distance, it makes a noticeable difference for A-form DNA or RNA structures.

Best regards,

Xiang-Jun

Offline maryatx3dna

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Re: minor and major grooves
« Reply #4 on: August 17, 2016, 01:37:55 pm »
ok sir it surely be cited.
thanking you

mary

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.