248
V. Poltev et al.
as compared to the other chain (Tables 2, 3 and Figs. 7, 8). DFT optimization using
M05-2X functional leads to the increase of base ring superposition in the dDMP,
which is in BI conformation, for both cdDMPs. The other chain experiences a slight
increase in the superposition for dApdT:dApdT (conformation family 110) and a
decrease for dApdC:dGpdT (conformation family 117). Both optimized structures
Table 2 Torsion angles and areas of superposition of base rings (S) for the initial and DFT optimized
conformations of dApdC:dGpdT with dApdC in BI conformation and dGpdC in conformation 117
cdDMPs
δ1
ε
ζ
α
β
γ
δ2
S(Å 2 )
(dApdC
132
195
254
344
166
3
148
2.42
dGpdT) 1
158
217
251
247
72
164
148
1.72
(dApdC
145
188
276
295
163
57
85
3.68
dGpdT) 2
144
191
269
264
70
168
157
0.94
(dApdC
143
188
279
296
166
56
89
3.51
dGpdT) 3
140
191
273
266
71
170
152
1.10
(dApdC
143
189
278
295
167
57
87
3.51
dGpdT) 4
139
194
271
265
73
169
150
1.00
(dApdC
139
176
274
298
163
57
123
3.14
dGpdT) 5
128
186
265
272
61
171
155
2.43
1) Initial structure extracted from UDJ060 duplex
2) GAUSSIAN-optimized structure using the M05-2X functional
3) ADF-optimized structure using dispersion correction (PW91-ulg functional)
4) ADF-optimized structure (PW91 functional)
5) AMBER-optimized structure (OL15 force field)
Table 3 Torsion angles and areas of superposition of base rings (S) for the initial and DFT optimized
conformations of dApdT:dTpdT with one chain being in BI conformation (upper line in the dual
row) and other chain being in 110 conformation (lower line in the dual row)
cdDMPs
δ1
ε
ζ
α
β
γ
δ2
S(Å 2 )
(dApdT
146
191
278
287
171
44
143
3.63
dApdT) 1
143
279
180
66
234
192
104
0.70
(dApdT
144
190
276
295
164
56
97
4.02
dApdT) 2
153
265
180
61
236
196
73
0.92
(dApdT
142
191
279
296
166
54
101
3.98
dApdT) 3
151
256
187
65
234
199
75
1.06
(dApdT
141
198
281
291
173
53
114
3.47
dApdT) 4
146
272
181
76
236
193
90
1.03
1) Initial structure extracted from 2MAV duplex
2) GAUSSIAN-optimized structure using the M05-2X functional
3) ADF-optimized structure using dispersion correction (PW91-ulg functional)
4) ADF-optimized structure (PW91 functional)
V. Poltev et al.
as compared to the other chain (Tables 2, 3 and Figs. 7, 8). DFT optimization using
M05-2X functional leads to the increase of base ring superposition in the dDMP,
which is in BI conformation, for both cdDMPs. The other chain experiences a slight
increase in the superposition for dApdT:dApdT (conformation family 110) and a
decrease for dApdC:dGpdT (conformation family 117). Both optimized structures
Table 2 Torsion angles and areas of superposition of base rings (S) for the initial and DFT optimized
conformations of dApdC:dGpdT with dApdC in BI conformation and dGpdC in conformation 117
cdDMPs
δ1
ε
ζ
α
β
γ
δ2
S(Å 2 )
(dApdC
132
195
254
344
166
3
148
2.42
dGpdT) 1
158
217
251
247
72
164
148
1.72
(dApdC
145
188
276
295
163
57
85
3.68
dGpdT) 2
144
191
269
264
70
168
157
0.94
(dApdC
143
188
279
296
166
56
89
3.51
dGpdT) 3
140
191
273
266
71
170
152
1.10
(dApdC
143
189
278
295
167
57
87
3.51
dGpdT) 4
139
194
271
265
73
169
150
1.00
(dApdC
139
176
274
298
163
57
123
3.14
dGpdT) 5
128
186
265
272
61
171
155
2.43
1) Initial structure extracted from UDJ060 duplex
2) GAUSSIAN-optimized structure using the M05-2X functional
3) ADF-optimized structure using dispersion correction (PW91-ulg functional)
4) ADF-optimized structure (PW91 functional)
5) AMBER-optimized structure (OL15 force field)
Table 3 Torsion angles and areas of superposition of base rings (S) for the initial and DFT optimized
conformations of dApdT:dTpdT with one chain being in BI conformation (upper line in the dual
row) and other chain being in 110 conformation (lower line in the dual row)
cdDMPs
δ1
ε
ζ
α
β
γ
δ2
S(Å 2 )
(dApdT
146
191
278
287
171
44
143
3.63
dApdT) 1
143
279
180
66
234
192
104
0.70
(dApdT
144
190
276
295
164
56
97
4.02
dApdT) 2
153
265
180
61
236
196
73
0.92
(dApdT
142
191
279
296
166
54
101
3.98
dApdT) 3
151
256
187
65
234
199
75
1.06
(dApdT
141
198
281
291
173
53
114
3.47
dApdT) 4
146
272
181
76
236
193
90
1.03
1) Initial structure extracted from 2MAV duplex
2) GAUSSIAN-optimized structure using the M05-2X functional
3) ADF-optimized structure using dispersion correction (PW91-ulg functional)
4) ADF-optimized structure (PW91 functional)