3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ilibarra on August 31, 2012, 05:05:06 pm

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper
Post by: ilibarra on August 31, 2012, 05:05:06 pm
Quote from: xiangjun on April 01, 2012, 10:31:26 am
The scheme of classifying a dinucleotide step into A-, B- or TA-DNA form is described in the 2003 NAR paper (http://nar.oxfordjournals.org/content/31/17/5108.full). More specifically, it is based on Zp and Zp(h); see Figure 5(c) linked below. For example, if Zp > 1.5 Å, then it is taken as A-DNA.

(http://nar.oxfordjournals.org/content/31/17/5108/F5.large.jpg)

Per your request, listed below is the exact definition for A-, B- and TA-DNA, as excerpted from 3DNA source code. Note the "sanity check" at the beginning; the empirical criteria try to ensure a right-handed duplex consisting of Watson-Crick bps and with reasonable geometry. Also bear in mind that the classification is intended to be indicative rather than conclusive.

Code: [Select]
if (dval_in_range(mtwist, 10.0, 60.0)  /* over-all twist average */
    && WC_info[i] && WC_info[i + 1]  /* WC geometry */
    && dval_in_range(twist_rise[i][1], 10.0, 60.0)  /* right-handed */
    && dval_in_range(twist_rise[i][2], 2.5, 5.5)  /* Rise in range */
    && dval_in_range(aveS[i][1], -5.0, -0.5)  /* Xp */
    && dval_in_range(aveS[i][2], 7.5, 10.0)  /* Yp */
    && dval_in_range(aveS[i][3], -2.0, 3.5)  /* Zp */
    && dval_in_range(aveH[i][1], -11.5, 2.5)  /* XpH */
    && dval_in_range(aveH[i][2], 1.5, 10.0)  /* YpH */
    && dval_in_range(aveH[i][3], -3.0, 9.0)) {  /* ZpH */
    if (aveS[i][3] >= 1.5)  /* A-form */
        strABT[i] = 1;
    else if (aveH[i][3] >= 4.0)  /* TA-form */
        strABT[i] = 3;
    else if (aveS[i][3] <= 0.5 && aveH[i][1] < 0.5)  /* B-form */
        strABT[i] = 2;  /* aveS[i][3] < 0.5 for C-DNA #47 */
}
HTH,

Xiang-Jun

I'd like to ask about the DNA set used for the analysis that is presented in Fig 5. in the NAR 2003 paper. Are those structures previously classified as A, B and TA DNA by other means (?) before doing the Zp and Zp(h) calculations to confirm their differences? Where can I look for the structures which were used? (I guess it is somewhere in reference 81, Patikoglou,G.A. et al (1999))

Thanks for the comments

Ignacio
Title: Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper
Post by: xiangjun on August 31, 2012, 05:38:14 pm
Quote
I'd like to ask about the DNA set used for the analysis that is presented in Fig 5. in the NAR 2003 paper. Are those structures previously classified as A, B and TA DNA by other means (?) before doing the Zp and Zp(h) calculations to confirm their differences? Where can I look for the structures which were used? (I guess it is somewhere in reference 81, Patikoglou,G.A. et al (1999))

Thanks for asking about the DNA datasets used in Figure 5 of the 3DNA 2003 NAR paper (http://nar.oxfordjournals.org/content/31/17/5108.full). Yes, the structures are previously assigned as A-, B- and TA-DNA by other means before we introduced Zp and Zp(h) to classify the three types of dinucleotide steps automatically. A- and B-DNA are based on conventional parameters (Slide/Roll, sugar puckers etc), as in the NDB, and the TA-DNA is mainly inspired by the work of Guzikevich‐Guerstein and Shakked (ref. 80 (http://www.ncbi.nlm.nih.gov/pubmed/8548452)):

Quote from: 3DNA 2003 NAR paper
A detailed structural analysis of two early examples of the TATA‐box DNA bound to the TATA‐box binding protein (TBP) (10,79) led Guzikevich‐Guerstein and Shakked (80) to propose that the 8 bp TATA‐box adopts a novel TA‐DNA conformation, different from either A or B DNA. The structures of many more such complexes have since been determined (81) and, as shown in Table 2 and Figure 5, all TATA‐box regions share similar conformational features.

So the complete list was not taken directly from somewhere in ref. 81 (http://www.ncbi.nlm.nih.gov/pubmed/10617571), but compiled specifically for the work. The actual structure list used in producing Figure 5 for the TA-DNA steps can be found in the thread "DNA standards/statistics using 3DNA (http://forum.x3dna.org/general-discussions/dna-standardsstatistics-using-3dna)", dated August 2006. For A-DNA and B-DNA structures used in Figure 5 of the 2003 paper, I need to locate my original record from (nearly) a decade ago -- I will write a post about my findings on the 3DNA homepage, possibly by next week.

HTH,

Xiang-Jun
Title: Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper
Post by: ilibarra on September 03, 2012, 10:44:45 pm
Thank you very much for the fast answers to the questions of this forum :D
Title: Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper
Post by: xiangjun on September 07, 2012, 02:15:17 pm
Thanks for your patience -- it took me quite some time to dig into my files used for the 2003 3DNA paper! Luckily, I got them, and the time has been well-worth spent :D.

Here are the details -- the whole datasets and scripts can be downloaded by following the link: 3DNA-NAR03-Fig5.tar.gz (http://x3dna.bio.columbia.edu/data/3DNA-NAR03-Fig5.tar.gz). Figure 5(a)-(c) generated with the scripts and data files are attached.


HTH,

Xiang-Jun

PS. As a matter of fact, the A- and B-DNA datasets are those used in Table 3 of the report on standard base reference (http://ndbserver.rutgers.edu/standards/standard_reference.html).

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.