Table 2: Comparison of backbone torsion angles and helicoidal parameters for average structures of each run after 20 ns MD simulation. Highlighted in bold are values for structure obtained by averaging all the three runs. Standard deviation is reported in brackets.
(a)

Helicoidal parameters
Duplex nameTwist (°)Roll (°)Tilt (°)Inclination (°)H.Ris (°)H.Twi (°)Groove width ( )

PNA:RNA_NMRa30.1 (4)4.9 (4.3)1.0 (3.3)9.0 (2.7)2.98 (0.2)30.6 (4.2)6.1 (0.5)
PNA:RNA_MDb23.7; 23.2
A-RNAc32122.815.83.33.8
PNA2 AVG tot24.5 (1.1)6.5 (1.6)1 (0.9)14.2 (0.6)2.79 (0.10)25.3 (1.1)6.8 (0.6)
PNA1 AVG tot24.9 (2.8)5.7 (2.2)0.9 (1.3)13 (1.1)2.77 (0.16)25.5 (2.9)6.8 (0.5)

(b)

Torsional PNA angles (in degrees)
N4–C5C5–CC–N1C2–C3C3–N4N4–C7

PNA:RNA_NMRa−84.980105.766−100.19.150.6
PNA2−79.9125.278.670.4−103−2.978
PNA1−81.3129131.569.5−103.3−2.178.5

(c)

Torsional RNA angles (in degrees)

PNA:RNA_NMRa−68.4111.7558.478.5−148.7−72.5−104.5
A-RNAc−521754279−146−75−157
miR20ad−99.1162.673.188.7−138−119.4−147.6
PNA2 AVG tot−84.4172.881.379.2−160.4−70.3−159.5
PNA1 AVG tot−88.8145.885.581.8−161.1−70.9−158.7

Calculated on the average of the 10 NMR structures of PDB structure 176D; bfrom [40]; cfrom [41]; dfrom [42].