Table 1. Experimental distances and distributions compared to estimated distances from a standard A-form RNA and to MD calculated distances for the investigated RNA secondary structures. The experimental error in the peak distance is much less than the distribution Δr and is estimated up to ± 0.1 nm (see text). Estimated distances are average of O–O, N–N, O–N and N–O distances.

	Sample	Δbp	Distances [nm]
			PELDOR		Model A-RNA	MD
			r	Δr	r	r	Δr
1	[6,16]duplex	10	3.07	0.2	2.82	2.80	0.17
2	[13,28]duplex	15	4.34	0.2	4.28
3	[16,31]duplex	15	4.32	0.2	4.28	4.27	0.22
4	[6,28]hairpin	18	5.14	0.3	5.11 a
5	[6,24]duplex	18	5.33	0.3	5.11
6	[6,28]duplex	22	6.32	0.4	6.19	6.07	0.25
7	[6,31]duplex	25	7.3	0.4	7.06	6.98	0.29
8	[3,31]duplex	28	8.1	0.5	7.91

^aHairpin distance was extracted from a model that contained only the double-stranded helix part of the hairpin, without the loop.