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Author Topic: Dinucleotide step parameters for "ideal" A-form RNA  (Read 6088 times)

Offline Guillermo Bermejo

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Dinucleotide step parameters for "ideal" A-form RNA
« on: September 11, 2015, 03:23:51 pm »
Hi,

I would like to know the consensus values for the dinucleotide step parameters of an ideal A-form RNA conformation. I've looked at the 3DNA 2003 paper (Lu & Olson, NAR, 2003, 31:5108-5121), where Table 1 shows the parameters for "A DNA". However, the reported Slide of -2 Angstroms seems large (in absolute value). For example, analysis of stems in a structural database compiled for my work yields an average of -1.6, and others have reported a value of -1.5 as a common Slide for A-RNA (Pingali et al., J Comput Aided Mol Des, 2014, 28:851-867).

Maybe I'm missing something... Could you point to a reference where the ideal or model A-form step parameters are listed?

Thanks!

Guillermo

Offline xiangjun

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Re: Dinucleotide step parameters for "ideal" A-form RNA
« Reply #1 on: September 11, 2015, 03:51:19 pm »
Hi Guillermo,

Thank for using 3DNA and posting on the 3DNA Forum.

Note that Table 1 of the 3DNA 2003 paper (Lu & Olson, NAR, 2003, 31:5108-5121) corresponds to Figure 4a-g, which has the following caption:

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Influence of non-zero Slide and Roll at sequential dimer steps on overall DNA helical conformation. Images generated with 3DNA building upon the principles of Calladine and Drew (42). The radii of the (dashed) circles in the upper row of images, defined by the loci of points from the helical axes (filled circles) to the base pair origin (open circles), correspond to the x-displacement. The values of dimeric Twist are adjusted, following equation 4, to keep the helical twist angle at 36°. The A-like model is highlighted in quotes to emphasize that the structure contains 10 rather than 11 residues per turn.

Thus the -2 Å Slide reported there is for idealized, regular structures based on the work of Calladine and Drew. In real x-ray crystal structure, Slide is indeed ~-1.5 Å. See Table 3 of the Olson et al. standard base reference report.

HTH,

Xiang-Jun
« Last Edit: September 11, 2015, 06:07:07 pm by xiangjun »

Offline Guillermo Bermejo

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Re: Dinucleotide step parameters for "ideal" A-form RNA
« Reply #2 on: September 11, 2015, 04:52:32 pm »
Thanks very much Xiang-Jun for your reply.  BTW, I started using 3DNA recently and I love it.

Thanks again,

Guillermo

Offline xiangjun

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Re: Dinucleotide step parameters for "ideal" A-form RNA
« Reply #3 on: September 11, 2015, 06:11:45 pm »
Hi Guillermo,

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BTW, I started using 3DNA recently and I love it.
Thank you for using 3DNA, and for your nice words about the software -- I certainly love to hear them :).

Do not forget to post any future 3DNA-related questions you may have on the Forum! Over the years, user feedback has been a key factor to drive the 3DNA project forward.

Best regards,

Xiang-Jun
« Last Edit: September 11, 2015, 06:16:55 pm by xiangjun »

 

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.