Table 13.

Inter-nucleotide distances (Å) in the 1YFV system. Experimental values are taken from Santa Lucia et al.^[89] Values in parenthesis reflect the distances most essential to the structural refinement. Error bars for the MD data are the RMS fluctuations over the entire time series.

Nucleotides	H1’-H8/H6		H2’-H8/H6		H3’-H8/H6
	Expt.	MD	Expt.	MD	Expt.	MD
G1-G2	4.7 ± 0.8	4.9 ± 0.2	2.6 ± 0.5	2.3 ± 0.2	> 2.4	3.2 ± 0.3
G2-C3	4.2 ± 0.8	4.8 ± 0.2	2.7 ± 0.5	2.1 ± 0.2	3.8 ± 0.8	3.3 ± 0.3
C3-G4	4.2 ± 0.8	5.2 ± 0.4	2.7 ± 0.5 (2.2)	2.8 ± 0.5	3.0 ± 0.6 (2.6)	2.6 ± 0.3
G4-A5	4.4 ± 0.8	4.5 ± 0.3	3.2 ± 0.6 (2.7)	2.5 ± 0.3	> 4.0 (4.5)	4.6 ± 0.3
A5-G6	4.5 ± 0.8	5.3 ± 0.4	3.1 ± 0.6 (3.3)	3.2 ± 0.6	2.7 ± 0.5 (2.2)	2.4 ± 0.2
G6-C7			2.3 ± 0.5	2.1 ± 0.2	3.1 ± 0.6	3.5 ± 0.3
C7-C8	3.8 ± 1.0	5.2 ± 0.3	2.3 ± 0.5	2.5 ± 0.4	3.5 ± 0.6	3.3 ± 0.3