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Questions and answers => General discussions (Q&As) => Topic started by: les on August 18, 2006, 02:58:39 am

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Title: DNA standards/statistics using 3DNA
Post by: les on August 18, 2006, 02:58:39 am

First, I would like to thank Xiang-Jun Lu and Wilma Olson for the 3DNA program, which certainly has filled a gap. My question concerns standard structures used with 3DNA.

In a paper by Xiang-Jun Lu & Wilma K. Olson about 3DNA, NAR 31(17), 5108-5121, the IDs of TA-DNA structures used are pointed to at a Rutgers site, but, the link didn't work for me. Is it possible to get this information?

Other statistics obtained using 3DNA might also be of interest so the question could be broader.

Best regards,
Les

Title: Re: DNA standards/statistics using 3DNA
Post by: xiangjun on August 18, 2006, 10:38:37 pm

Dear Les,

Thanks for your kind words regarding 3DNA. It's been my pleasure to see it so widely accepted by the community. Over the years, I have taken each user's question as an opportunity to improve it.

Now back to your question. I have dug out the TA-DNA structures used in our 3DNA paper, and they are as follows:

Code: [Select]

pd0070, pd0112, pd0154, pd0155, pd0156 pd0157, pd0158, pd0159, pd0160,
pd0161, pd0162, pd0163, pd0164, pdr031 pdt009, pdt012, pdt024, pdt025,
pdt032, pdt034, pdt036

This directory contains TATA box segments. It is normally 8-bp long, and
has the sequence: T-A-T-A-@-A-@-N. There are two kinks at the terminal
steps.

* means non-WC base-pair which is eliminated from further analysis

NDB ID  ##     Sequence      Res(A)  R-fac(%) chainID and residue range
--------------------------------------------------------------------
pd0070  01  T-T-T-A-A-A-T-A   2.4     20.0   C 1410 1417 D 1432 1439
                           
pd0112  02  T-A-T-A-A-A-A-G   2.65    23.1   K 8 15 L 105 112
        03  T-A-T-A-A-A-A-G                  C 8 15 D 105 112
        04  T-A-T-A-A-A-A-G                  G 8 15 H 105 112
        05  T-A-T-A-A-A-A-G                  O 8 15 P 105 112
        06  T-A-T-A-A-A-A-G                  S 8 15 T 105 112
                                      
pd0154  07  T-A-T-A-A-A-A-T   1.86    21.0   C 203 210 D 219 226
        08  T-A-T-A-A-A-A-T                  E 203 210 F 219 226
                                   
pd0155  09  T-A-T-A-A-G-A-G*  1.93    19.6   C 203 209 D 220 226
        10  T-A-T-A-A-G-A-G*                 E 203 209 F 220 226
   
pd0156  11  T-A-T-A-A-T-A-G*  2.1     19.3   C 203 209 D 220 226
        12  T-A-T-A-A-T-A-G*                 E 203 209 F 220 226
                                   
pd0157  13  T-A-T-A-T-A-A-G*  2.3     19.4   C 203 209 D 220 226
        14  T-A-T-A-T-A-A-G*                 E 203 209 F 220 226
                                   
pd0158  15  T-A-T-T-A-A-A-G*  2.1     19.4   C 203 209 D 220 226
        16  T-A-T-T-A-A-A-G*                 E 203 209 F 220 226
                                   
pd0159  17  T-A-C-A-A-A-A-G*  1.9     20.9   C 203 209 D 220 226
        18  T-A-C-A-A-A-A-G*                 E 203 209 F 220 226
   
pd0160  19  T-T-T-A-A-A-A-G*  1.8     19.3   C 203 209 D 220 226
        20  T-T-T-A-A-A-A-G*                 E 203 209 F 220 226
                                      
pd0161  21  T-A-T-A-A-A-T-G*  2.23    19.1   C 203 209 D 220 226
        22  T-A-T-A-A-A-T-G*                 E 203 209 F 220 226
                                      
pd0162  23  A-A-T-A-A-A-A-G*  2.3     18.2   C 203 209 D 220 226
        24  A-A-T-A-A-A-A-G*                 E 203 209 F 220 226
                                      
pd0163  25  T-A-T-A-A-A-A-G   1.9     19.7   C 203 210 D 219 226
        26  T-A-T-A-A-A-A-G                  E 203 210 F 219 226
                                      
pd0164  27  T-A-T-A-A-A-C*G*  1.95    19.9   C 203 208 D 221 226
        28  T-A-T-A-A-A-C*G*                 E 203 208 F 221 226
                                      
pdr031  29  T-T-T-t-t-A-A-A   2.1     21.2   C 1408 1415 E 1420 1427
                                      
pdt009  30  T-A-T-A-A-A-A-G   2.25    20.2   A 203 210 B 305 312
        31  T-A-T-A-A-A-A-G                  C 403 410 D 505 512
                                      
pdt012  32  T-A-T-A-T-A-A-A   1.8     20.1   C 2 9 C 21 28
        33  T-A-T-A-T-A-A-A                  D 2 9 D 21 28
                                      
pdt024  34  T-A-T-A-T-A-T-A   2.9     21.4   B 103 110 C 115 122
                                      
pdt025  35  T-A-T-A-A-A-A-G   1.9     19.4   C 203 210 D 219 226
        36  T-A-T-A-A-A-A-G                  E 303 310 F 319 326
                                      
pdt032  37  T-A-T-A-A-A-A-G   2.7     21.5   C 4 11 D 106 113
                                      
pdt034  38  T-A-T-A-A-A-A-G   1.9     18.9   B 5 12 C 105 112
                                      
pdt036  39  T-A-T-A-A-A-A-C   2.5     23.5   E 9 16 F 1 8

When time permits, I will put the A-DNA and B-DNA structures used in 3DNA paper on 3DNA wiki as well.

HTH,

Xiang-Jun

PS. See the thread "Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper (http://forum.x3dna.org/general-discussions/datasets-and-scripts-for-reproducing-figure-5-of-the-3dna-nar03-paper/)" for final details [added 2012-09-07].

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University

3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: les on August 18, 2006, 02:58:39 am