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Questions and answers > General discussions (Q&As)
Classifying structures into A, B , AB, TA .. types
Puru@1998:
Hello
I have been working on RNA/DNA hybrids with conformational parameters, along with DNA and RNA duplexes.
I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?
Sincerely,
Puru
mauricio esguerra:
Hej Puru,
Perhaps a look at the original reference of Xiang-Jun Lu for 3DNA, say, Figure 5 of his 2003 paper in Nucleic Acids Research will come in handy.
http://dx.doi.org/10.1093/nar/gkg680
In that figure Inclination vs. x-displacement, Roll vs. Slide, and Zp(h) vs. Zp are plotted and are quite neat indicators of the conformational types of nucleic acids.
There's even an older 2000 paper by the same first author, and the creator or 3DNA, which predates 3DNA. It is also quite the recommended read.
http://dx.doi.org/10.1006/jmbi.2000.3690
All of the parameters needed to do the figures in the two mentioned papers are easily obtained using 3DNA.
Hope this helps,
Mauricio
xiangjun:
Thanks, Mauricio, for chiming in and for your nice words about my early publications.
--- Quote from: Puru ---I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?
--- End quote ---
Could you please clarify your question, preferably with a concrete example?
Xiang-Jun
Puru@1998:
Hello. Thank you for your responses.
I will clarify my questions to the best of my ability.
I am trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B) ..in this manner. I was wondering if 3dna has a way of accomplishing this without me having to do it manually say for a database of 300 structures of DNA/DNA and RNA/RNA duplexes that I have created.
Examples: step Xp Yp Zp XpH YpH ZpH Form
1 GG/CC -2.93 8.97 0.37 -3.31 8.93 0.93 B
2 GT/AC -3.35 9.11 -0.39 -4.65 9.11 0.27 B
3 TG/CA -2.75 8.65 -0.88 0.06 8.42 -2.19 B
4 GC/GC -3.75 8.88 -1.02 -4.46 8.86 1.15 B
5 CA/TG -2.21 8.39 -0.80 0.87 8.11 -2.24
6 AA/TT -3.16 8.72 -0.76 -3.15 8.69 -1.08 B
7 AC/GT -3.34 8.80 0.30 -4.58 8.79 -0.36 B
8 CA/TG -3.15 8.59 0.82 -5.42 7.85 3.62
9 AA/TT -3.40 8.91 -0.05 -5.18 8.77 1.57 B
10 AA/TT -2.85 9.21 0.49 -4.46 8.93 2.31 B
11 AT/AT -2.73 9.23 0.37 -5.90 8.10 4.48
12 TT/AA -3.06 8.49 0.75 -7.77 2.66 8.09
13 TG/CA -1.93 8.53 -1.20 -1.73 8.42 1.80
14 GA/TC -3.71 8.29 -1.70 -1.39 8.33 -1.77
15 AT/AT -3.33 8.91 0.01 -3.85 8.89 -0.62 B
16 TA/TA -3.07 8.68 0.30 -3.26 8.62 -1.09 B
17 AA/TT -3.23 8.99 -0.12 -3.62 8.93 -1.05 B
18 AG/CT -2.99 8.80 -0.12 -4.25 8.76 0.81 B
19 GC/GC -2.88 8.98 -0.05 -2.91 8.98 -0.13 B
20 CA/TG --- --- --- --- --- --- ---
21 AA/TT --- --- --- --- --- --- ---
22 AT/AT -1.31 5.67 -0.75 -1.12 5.67 -0.38
23 TG/CA -3.05 9.04 -0.43 -1.94 9.05 -0.15 B
24 GC/GC -3.22 9.12 -0.18 -3.87 9.12 0.02 B
25 CT/AG -3.15 8.71 0.12 -4.40 8.67 0.80 B
26 TT/AA -3.20 9.07 -0.14 -3.66 9.01 -1.00 B
27 TT/AA -3.31 9.00 -0.28 -4.03 9.00 -0.28 B
28 TT/AA -3.32 8.90 -0.38 -3.06 8.75 -1.69 B
29 TT/AA -2.84 8.83 -0.02 -2.70 8.77 -0.99 B
30 TT/AA -3.17 8.80 -0.39 -4.01 8.81 -0.16 B
31 TG/CA -2.68 8.86 -0.39 -2.17 8.73 1.56 B
32 GG/CC -2.62 8.93 0.55 -4.88 8.43 3.01
33 GC/GC -3.01 9.06 0.57 -4.46 8.93 1.66
About 63 percent B so, B- Like
Structure 1ihf.pdb
step Xp Yp Zp XpH YpH ZpH Form
1 Ug/gA -0.59 1.90 -10.29 -1.26 -5.96 -8.21
2 gg/gg -0.03 11.87 -0.05 -0.04 11.87 -0.05
3 gA/Ug 4.30 6.48 0.76 4.86 6.47 0.71
4 AG/GU --- --- --- --- --- --- ---
5 GA/UG --- --- --- --- --- --- ---
6 AG/GU --- --- --- --- --- --- ---
7 GA/UG 0.91 7.95 -3.89 0.95 7.96 -3.89
8 AU/AU --- --- --- --- --- --- ---
9 UG/GA 4.86 -3.16 -3.09 3.46 -5.61 -2.45
10 GG/GG 2.86 -8.07 9.47 0.69 -11.79 7.22
11 GU/UG -0.70 -5.57 0.33 -0.39 -5.58 -0.02
12 UA/UU 4.87 4.65 9.91 6.37 4.62 8.66
13 Ag/gU --- --- --- --- --- --- ---
14 gU/Ag --- --- --- --- --- --- ---
15 UG/GA 4.76 -3.15 -3.07 3.40 -5.68 -2.41
16 GU/UG -0.69 -0.62 3.16 3.87 0.05 -5.38
17 UG/GU -1.13 9.00 12.68 -1.60 9.15 12.56
18 GU/UG -2.66 2.33 7.98 -3.11 -1.49 5.97
19 UA/UU 1.44 7.36 8.41 1.48 7.36 8.39
20 Ag/gU --- --- --- --- --- --- ---
21 gG/Gg -1.88 -0.50 6.72 -3.52 -0.95 6.73
22 GG/GG 2.93 -8.32 9.69 0.64 -11.88 7.20
23 GU/UG -0.93 -5.19 0.60 -0.36 -5.24 0.05
(this structure has x on for a step without a continuous backbone- from the DSSR output; 3dna just leaves them blank)
step Xp Yp Zp XpH YpH ZpH Form
1 ga/TC -2.77 8.59 0.69 -3.28 8.62 0.28
2 ac/GT -2.49 8.71 1.70 -4.62 8.57 2.22
3 ca/TG -3.29 8.69 1.01 -7.71 7.93 3.84
4 ac/GT -3.02 9.01 1.11 -8.02 8.96 1.50
5 cc/GG -1.93 8.22 2.51 -5.41 7.78 3.66 A
6 cu/AG -2.26 8.95 1.99 -6.31 9.06 1.61 A
7 ug/CA -2.51 8.67 1.19 -4.74 8.70 1.07
8 ga/uC -2.43 8.87 1.41 -6.30 7.97 4.14
9 au/Au -2.90 8.63 0.53 -5.39 8.55 1.15
10 uu/AA -2.76 8.87 1.25 -8.18 8.07 3.92
11 uc/GA -2.38 8.52 1.92 -5.00 8.39 2.38
9 percent A..?
3DNA has been incredible to use so far, very multi-dimensional and comprehensive.
Thank you.
Puru@1998:
Hello.
I was wondering if you had a response regarding my post above.
Thanks.
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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.
