Exploitation of a Very Small Peptide Nucleic Acid as a New Inhibitor of miR-509-3p Involved in the Regulation of Cystic Fibrosis Disease-Gene Expression
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 name
Twist (°)
Roll (°)
Tilt (°)
Inclination (°)
H.Ris (°)
H.Twi (°)
Groove width ()
PNA:RNA_NMRa
30.1 (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_MDb
23.7; 23.2
A-RNAc
32
12
2.8
15.8
3.3
3.8
PNA2 AVG tot
24.5 (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 tot
24.9 (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–C5
C5–C
C–N1
C2–C3
C3–N4
N4–C7
PNA:RNA_NMRa
−84.9
80
105.7
66
−100.1
9.1
50.6
PNA2
−79.9
125.2
78.6
70.4
−103
−2.9
78
PNA1
−81.3
129
131.5
69.5
−103.3
−2.1
78.5
(c)
Torsional RNA angles (in degrees)
PNA:RNA_NMRa
−68.4
111.75
58.4
78.5
−148.7
−72.5
−104.5
A-RNAc
−52
175
42
79
−146
−75
−157
miR20ad
−99.1
162.6
73.1
88.7
−138
−119.4
−147.6
PNA2 AVG tot
−84.4
172.8
81.3
79.2
−160.4
−70.3
−159.5
PNA1 AVG tot
−88.8
145.8
85.5
81.8
−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].
