Table 2.

Base pairing changes detected in the standard simulations performed with the X-ray H40 UAA/GAA structure.

Simulation name	sheared A/G pair		reverse Hoogsteen U/A pair
	A(N7)-G(N2) H-bond	A(N6)-G(N3) H-bond	U(O2)-A(N6) H-bond	U(N3)-A(N7) H-bond
MD_Ec_99	75–78 ns oe	33–40 ns oe	stable	89.2–90.1 ns oe
	133–297 ns d	65–78 ns oe		at 101 d
		133–297 ns d
MD_Ec_bsc0	f	Stable	stable	18.5–23.2 ns oe
				41.3–46.8 ns oe
				at 65 ns d
MD_Hm_99	at 150 ns d	39–45 ns oe	stable	56–81 ns oe
		45–97 f
		97–109 oe
		150 ns d
MD_Hm_bsc0	1–5 ns oe	f	stable	5–15 ns ns oe
	90–94 ns oe			26–37 ns oe
				75–96 ns oe
MD_Dr_99	stable	f	stable	at 7 ns d
MD_Dr_bsc0	stable	f	stable	At 30 ns d
MD_Tt_99	63–65 ns oe	63–65 ns oe	stable	70–122 ns oe
MD_Tt_bsc0	58–69 ns oe	58–69 ns oe	stable	13–17 ns ns oe
				24–32 ns oe
				60–78 ns oe
				83–96 ns oe
MD_Ec_K1	f	stable	77–80 ns oe	4–22 ns oe
				77–80 ns oe
				96–98 ns oe
MD_Ec_K2	stable	f	stable	11–28 ns oe
MD_Ec_K3	stable	stable	stable	8–9 ns oe
				16–20 ns oe

“oe”, “d” and “f” marks stand for temporary opening, disruption (till the end of the simulation) and considerable fluctuations, respectively.