Skip to main content
. Author manuscript; available in PMC: 2011 Nov 19.
Published in final edited form as: J Mol Biol. 2010 Sep 25;404(1):138–157. doi: 10.1016/j.jmb.2010.09.043

Table 3.

Changes in phosphate SASA accompanying RNA unfoldinga

RNA PO2 SASA
(native), Å2 		PO2 SASA
(unfolded), Å2 		Δ(SASA), Å2 estimated m-value,
kcal/mol/m
58mer RNA 3136 3534–4007 398 or 871 0.99 or 2.16
tar-tar* 1968 1860 – 2108 −92 or 141 −0.23 or 0.35
TLR 758 (receptor) 388 (GAAA) 722 (receptor) 391 (GAAA) −67 −0.17
A-riboswitch 4768 4401–4991 −367 or 223 −0.91 or 0.55
a

Solvent accessible surface areas of backbone phosphate (phosphorus and the two non-bridging oxygens) for native RNA structures were calculated from PDB files specified in the legend to Figure 8. For TLR RNA, surface areas corresponding to the receptor (nucleotides U5 – G9 and C34 – G39 for chain A; U48 – G52 and C77 – G82 for chain B) and the tetraloop hairpin (nucleotides G19 – C24 for chain A; G62 – C67 for chain B) are reported separately. The unfolded TLR RNA surface areas are derived from models as described in the text. Note that these numbers are for each subunit whereas the total change in SASA is for the complex. The values given for unfolded tar-tar*, A-riboswitch and 58mer RNA used the per-nucleotide SASA previously calculated for canonical A-form RNA (the smaller value) or single-stranded RNA.12 The contribution of phosphate exposure to the m-value for RNA unfolding in TMAO were calculated using the proportionality 2.48 cal/Å2/m.