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I´m analyzing an double helix RNA with a modified nucleotide. The effect of the modification pushes one of the bases but doesnt affect complementary one. stragger, proppeler and Buckle are very affected. Since it affects only one base of the base pair I dont know if it is correct two analyze roll and tilt. May be its a wrong average of a non-averageble structure.
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Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 2.86 N1 - N3 2.90 N2 - O2 2.81
2 A-----U [2] N6 - O4 3.03 N1 - N3 2.90
3 A-----U [2] N6 - O4 2.98 N1 - N3 2.91
4 A-----U [2] N6 - O4 2.94 N1 - N3 2.95
5 A-----U [2] N6 - O4 2.89 N1 - N3 2.96
6 G-----C [3] O6 - N4 2.95 N1 - N3 2.93 N2 - O2 2.85
7 A-----U [2] N6 - O4 3.05 N1 - N3 2.92
8 A-----U [2] N6 - O4 3.03 N1 - N3 2.94
9 A-----U [2] N6 - O4 2.96 N1 - N3 2.92
10 G-----C [3] O6 - N4 2.91 N1 - N3 2.91 N2 - O2 2.80
11 A-----U [2] N6 - O4 3.00 N1 - N3 2.89
12 A-----U [2] N6 - O4 2.95 N1 - N3 2.96
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Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.23 -0.18 -0.63 -20.29 -2.28 -0.66
2 A-U 0.09 -0.04 -0.48 -13.64 -10.06 4.26
3 A-U 0.06 -0.06 -0.53 -11.24 -12.42 2.82
4 A-U 0.09 -0.03 -0.62 -13.46 -13.99 0.86
5 A-U 0.18 0.01 -0.56 -15.56 -12.75 -1.66
6 G-C -0.05 -0.03 -0.69 -25.26 -19.76 2.36
7 A-U 0.06 0.01 -0.35 -7.49 -7.94 4.36
8 A-U 0.14 -0.00 -0.49 -8.36 -11.15 3.57
9 A-U 0.09 -0.04 -0.34 -6.42 -10.45 1.32
10 G-C -0.11 -0.13 -0.33 -9.45 -12.75 1.08
11 A-U 0.08 -0.08 -0.36 -9.60 -12.41 3.48
12 A-U 0.16 -0.09 -0.35 -1.29 -11.67 0.95
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ave. 0.05 -0.06 -0.48 -11.84 -11.47 1.89
s.d. 0.12 0.06 0.13 6.42 4.05 1.91
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Thus, from what I have in hand, nothing appears (to me) really unusual here. Of course, it would also be helpful to analyze your structure with other programs, e.g., Curves, to see what you get.Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.