Table 5.

Structural parameters of single-strand PNA and PNA/RNA hybrid from MD simulations. SD is the standard deviation between all bases and conformations. The parameters for several experimental structures are also listed for comparison. Ax-bend is the total axis bending angle divided by the number of base steps. The parameters were calculated by Curves+.⁸⁹

		Expt.			MD
	DNA/RNA	PNA/RNA		PNA/PNA	PNA		PNA/RNA
	(PDB: 1PJG)	(PDB: 176D)	(PDB: 5EMF)	(PDB: 1PUP)	Mean	SD	Mean	SD
Xdisp (Å)	−3.41	−3.60	−5.81	−7.87	−5.31	2.20	−6.01	0.85
Ydisp (Å)	−0.56	0.85	1.76	−0.05	1.23	2.34	0.95	0.78
Incline (°)	12.90	7.20	11.10	7.50	17.73	12.23	12.58	6.29
Tip (°)	1.40	−2.40	−0.70	−0.50	6.76	14.53	3.63	5.79
Ax-bend (°)	2.78	0.72	1.74	1.24	2.63	1.45	1.08	0.56
Shift (Å)	0.02	−0.42	−0.88	0.03	−1.11	1.79	−0.65	0.50
Slide (Å)	−1.20	−1.61	−2.08	−2.51	−1.86	0.92	−2.19	0.40
Rise (Å)	3.23	3.39	3.29	3.35	3.30	0.58	3.23	0.35
Tilt (°)	−0.90	2.60	0.00	0.30	−2.34	10.26	−1.53	6.11
Roll (°)	7.30	3.70	5.00	2.70	7.02	7.72	5.89	5.87
Twist (°)	31.40	30.00	24.50	20.00	26.69	17.41	25.22	4.51
Buckle (°)	−5.50	1.80	1.70	0.10	-	-	−1.36	6.83
Propeller (°)	−10.50	−15.30	−8.80	−8.10	-	-	−6.07	6.80
Opening (°)	3.20	2.60	1.20	0.40	-	-	1.17	3.60