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1

General discussions (Q&As) / Re: Dinucleotide step parameters for "ideal" A-form RNA

« 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

2

General discussions (Q&As) / 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