Table 1.

WC base-pairing distances and solvent accessibilities of the four systems at selected points along the base-flipping pathway

Extent of flipping	Aqueous	Binary, open	Binary, closed	Ternary
N1-N3 hydrogen bonding distances for the target C-orphan G base pair
Double-helical WC	2.97  ± 0.09	2.95  ± 0.09	4.33  ± 0.92	4.71  ± 0.28
50% barrier	3.77  ± 0.21	3.74  ± 0.20	4.74  ± 0.48	7.34  ± 0.65
100% barrier	9.30  ± 2.11	7.98  ± 0.56	8.24  ± 0.50	9.60  ± 0.59
Flipped state	15.53  ± 0.75	18.04  ± 0.33	18.53  ± 0.55	18.56  ± 0.36
Minor barrier	5.27  ± 0.29	6.36  ± 1.02	5.28  ± 0.21	2.98  ± 0.11
Solvent accessibilities of the DNA central tribase
Double-helical WC	866  ± 12	656  ± 25	427  ± 20	472  ± 16
50% barrier	869  ± 17	607  ± 17	492  ± 12	487  ± 13
100% barrier	976  ± 47	618  ± 21	485  ± 14	423  ± 21
Flipped state	1152  ± 31	604  ± 17	385  ± 16	367  ± 12
Minor barrier	934  ± 17	656  ± 40	459  ± 26	439  ± 13

Distances are given in Å, solvent accessibilities are given in Ų. Errors represent rms fluctuations. Double-helical WC corresponds to a pseudodihedral value of x = 10° in Fig. 1E; 50% barrier corresponds to 340°; 100% barrier corresponds to the maxima at 315° for DNA in aqueous solution and the open-binary complex for major groove flipping; the flipped state corresponds to 195°, and the minor groove barrier is the approximate location of the barrier for DNA in aqueous solution and the open-binary flipping profiles at 40°.