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Questions and answers => General discussions (Q&As) => Topic started by: Puru@1998 on June 19, 2018, 03:42:05 pm

Title: Classifying structures into A, B , AB, TA .. types
Post by: Puru@1998 on June 19, 2018, 03:42:05 pm: 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
Title: Re: Classifying structures into A, B , AB, TA .. types
Post by: mauricio esguerra on June 20, 2018, 04:10:54 am: 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 (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 (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
Title: Re: Classifying structures into A, B , AB, TA .. types
Post by: xiangjun on June 20, 2018, 01:29:06 pm: 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)?

Could you please clarify your question, preferably with a concrete example?

Xiang-Jun
Title: Re: Classifying structures into A, B , AB, TA .. types
Post by: Puru@1998 on June 22, 2018, 01:26:17 pm: 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.
Title: Re: Classifying structures into A, B , AB, TA .. types
Post by: Puru@1998 on July 04, 2018, 11:40:08 pm: Hello.

I was wondering if you had a response regarding my post above.

Thanks.
Title: Re: Classifying structures into A, B , AB, TA .. types
Post by: xiangjun on July 05, 2018, 06:24:13 am: Sorry for being late in responding to your follow-up post on June 22, 2018. I was on a trip to China for the whole month of June and slightly beyond, and I was constrained by my schedule and limited internet access.

Now back to your question, I am confused by what you mean by the following quantitative measures:

Quote
trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B)...
About 63 percent B so, B- Like...
9 percent A..?

The classification of a DNA dinucleotide step as A-, B- or TA-type is (mostly) based on Zp. See the 2000 A-DNA motif paper in JMB (https://www.ncbi.nlm.nih.gov/pubmed/10891271), and the 3DNA source code (ana_fncs.c) for further details.

Best regards,

Xiang-Jun