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