. Author manuscript; available in PMC: 2010 Mar 1.

Published in final edited form as: Methods. 2009 Jan 14;47(3):177–186. doi: 10.1016/j.ymeth.2008.12.003

Table 3.

Distribution of paired bases in RNA helical structures.

Helical location^†	Base-pair^‡
Helical location^†	All	G·C__WC	A·U__WC	G·U__w	G·A__s	A·U__H	U·U__w	G·A__WC
Interior
intact	0.62	0.62	0.75	0.63	0.34	0.05	0.74	0.25
‘nick’	0.20	0.20	0.16	0.26	0.25	0.29	0.13	0.66
‘insert’	0.02	0.01	0.01	0.00	0.03	0.42	0.03	0.01
Terminus
intact	0.13	0.15	0.07	0.10	0.33	0.05	0.10	0.06
‘insert’	0.02	0.01	0.01	0.01	0.05	0.19	0	0.02

^†

Fraction of the specified nucleotide association in different structural contexts within the arrays of stacked base pairs in high-resolution RNA structures: intact – sequential bases laterally attached to D-ribose sugars that are linked, in turn, via a normal 3′-5′ covalent phosphodiester linkage; ‘nick’ – bases or base pairs attached to sequentially distant sugars and thereby ‘broken’ by the folding of the nucleotide backbone; insert – single bases or base pairs that resemble intercalating ligands by stacking against or between chemically intact base-paired steps

^‡

Base-pair subscripts correspond to the designations in Table 2: Watson-Crick (WC); w (wobble); H (Hoogsteen). ‘All’ refers to the 17,328 pairs of bases formed from all combinations of A, U, G, and C (Table 1).