TABLE 1.

Summary of abbreviations of all structures analyzed in this study

Abbreviation	Description	Trajectory length
Lateral loops
K	X-ray structure by Kang (Kang et al., 1992), PDB code 1D59
K-M	Conventional MD simulation started from K, Na+ ions	2.5 ns
K-M(K+)	Conventional MD simulation started from K, K+ ions	2.5 ns
C1	Conformational search CICADA structure 1 (the lowest energy one)
C2	CICADA structure 2
C3	CICADA structure 3
C4	CICADA structure 4, with MD-relaxed quartet geometry
C1-M	Conventional MD simulation started from structure C1	3 ns
C2-M	Conventional MD simulation started from structure C2	3 ns
C3-M	Conventional MD simulation started from structure C3	3 ns
C4-M	Conventional MD simulation started from structure C4	3 ns
C1-L	LES simulation started from structure C1, parm99	6 ns
C1-L-M	Conventional MD simulation started from the C1-L structure (last 0.5-ns average)	3 ns
K-M-L	LES simulation started from structure K-M, parm99	6 ns
K-M-L-M	Conventional MD simulation started from K-M-L structure (last 0.5-ns average)	3 ns
Diagonal loops
Fdiag	NMR structure by Feigon (Schultze et al., 1994; Smith and Feigon, 1992), PDB code 156D
Ndiag	X-ray structure by Neidle (Haider et al., 2002), PDB code 1JRN
Hdiag	X-ray structure by Horvath (Horvath and Schultz, 2001), PDB code1JB7
Fdiag-M	Conventional MD started from structure Fdiag	10 ns
Hdiag-M	Conventional MD started from structure Hdiag with four integral Na+ cations	5 ns
Ndiag-M	Conventional MD started from structure Ndiag with five integral Na+ cations	5 ns
Ndiag-M(K+)	Conventional MD started from structure Ndiag, with five integral cations, in presence of K+	5 ns
Fdiag-L	LES run started from structure Fdiag, parm99	6 ns
Fdiag-L-M	Conventional MD simulation started from the Fdiag-L structure (last 0.5-ns average)	3 ns

MD simulations were performed with parm94 parameter set if not specified otherwise.