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Author Topic: Standards on defining nucleic acid structural parameters  (Read 3015 times)

Offline xiangjun

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Standards on defining nucleic acid structural parameters
« on: January 10, 2012, 07:54:25 pm »
There are currently two consecutive standards on the nomenclature and definition of nucleic acid structural parameters, the initial 1989 Cambridge Convention, and the 1999/2001 Tsukuba Report (standard base-reference frame).

The 1989 Cambridge Convention

The 1989 EMBO Workshop (held at Cambridge, England) provided the first systemic "definitions and nomenclature of nucleic acid structure parameters" [Dickerson et al. (1989), Nucleic Acids Res., 17(5), 1797-803]. Thereafter, several analysis programs were updated or created (most notably Curves from Richard Lavery and NewHelix/FreeHelix from Richard Dickerson), following the loosely defined convention. Even though the parameters are now named the same, the different programs can provide conflicting numerical values, especially for strongly distorted structures. See, for example, Werner et al. (1996) "Intercalation, DNA kinking, and the control of transcription" [Science, 271(5250), 778-84].


The 1999 Tsukuba Workshop

Our efforts in "resolving the discrepancies among nucleic acid conformational analyses" uncovered the source of the disparate descriptions from commonly used software programs:

Quote
Growing interest in understanding the relationship between the global folding of nucleic acids and the sequence-dependent structure of individual base-pair steps has stimulated the development of new mathematical methods to define the geometry of the constituent base-pairs. Several approaches, designed to meet guidelines set by the nucleic acid community, permit rigorous comparative analyses of different three-dimensional structures, as well as allow for reconstruction of chain molecules at the base-pair level. The different computer programs, however, yield inconsistent descriptions of chain conformation. Here we report our own implementation of seven algorithms used to determine base-pair and dimer step parameters. Aside from reproducing the results of individual programs, we uncover the reasons why the different algorithms come to conflicting structural interpretations. The choice of mathematics has only a limited effect on the computed parameters, even in highly deformed duplexes. The results are much more sensitive to the choice of reference frame. The disparate schemes yield very similar conformational descriptions if the calculations are based on a common reference frame. The current positioning of reference frames at the inner and outer edges of complementary bases exaggerates the rise at distorted dimer steps, and points to the need for a carefully defined conformational standard.

This work laid the foundation for the standardization of the base-pair parameters in the 1999 Tsukuba Workshop on Nucleic Acid Structure and Interactions. Following public review and discussion, and final approval by the IUBMB Nomenclature Committee, the standard base-reference frame paper came out in 2001 [PDF from the Nucleic Acids Database (NDB)]. From the initiation to its completion, the standardization was made possible by the NDB project, led by Helen Berman.

While not a participant of the 1999 Tsukuba Workshop, I was nevertheless heavily involved in the preparation of the final report. In the following posts at this section, I am planning to provide full data files and scripts so the Figures and Tables can be re-generated. In addition to serving as learning materials for new comers to the field of nucleic acid structures, the details should also be of interest to seasoned practitioners to watch for the caveats. From my own perspective, the work is directly relevant to the automatic identification and classification of non-canonical base pairs in RNA structures, among other possible applications already implemented in or to be added to 3DNA.

To the best of my knowledge, currently only 3DNA and Curves+ conform to the standard base-reference frame; as a result, the structural parameters (for Watson-Crick base-pair duplexes) calculated by the two programs are very similar.

Related PDF Documents
« Last Edit: September 18, 2012, 03:38:01 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Offline bciezah1

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Re: Standards on defining nucleic acid structural parameters
« Reply #1 on: April 02, 2017, 11:59:10 am »
Hello,

I have been reading your post about Standards on defining nucleic acid structural parameters, regarding this I have a question. There is also a standard value for this parameters in DNA? For example, in my case I am interested in the propeller twist in DNA. I wonder if there is a standard value of propeller twist for the pair A-T that I can use to compare with my data. I mean for example, I am studying the conformation of a sequence of DNA when interact with a protein...here the pairs A-T could show a value of -20 for example...I wonder is there is a standard value for this pair A-T to compare with my results to calculate a deviation. The same for the other one G-C.

Thank you so much,

Basilio.
=)

Offline xiangjun

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Re: Standards on defining nucleic acid structural parameters
« Reply #2 on: April 02, 2017, 12:21:49 pm »
The report "A standard reference frame for the description of nucleic acid base-pair geometry." [the original PDF at the NDB server] contains a table (Table 3) that lists average values and dispersion of base-pair parameters in high resolution A-and B-DNA crystal structures. Among which, propeller is included.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Offline bciezah1

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Re: Standards on defining nucleic acid structural parameters
« Reply #3 on: April 02, 2017, 12:39:08 pm »
Dear Xiang-Jun,

Thank you for your soon answer. I found the paper, and I found the table. I could see there is not a difference between a pair A-T and G-C. I wonder if this is because they analyzed separately the propeller in A-T and G-C, but they did not find difference or they just calculated the average propeller twist for all the structures. Well I just wanted to share this doubt with you. I will read in detail the paper.

Thank you so much,

Basilio.
=)

Offline xiangjun

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Re: Standards on defining nucleic acid structural parameters
« Reply #4 on: April 02, 2017, 12:43:34 pm »
Quote
I could see there is not a difference between a pair A-T and G-C.

Good catch! The table was compiled by combining A–T and G–C pairs together. In reality, there is some difference in propeller between the two pairs: A–T has slightly larger (more negative) propeller than G–C. At this moment, I cannot trace back the original data I used for Table 3 of the report.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline bciezah1

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Re: Standards on defining nucleic acid structural parameters
« Reply #5 on: April 02, 2017, 12:53:48 pm »
I see...I understand. Well I can try to calculate them again (because the crystal structures are listed in the table) and see the difference between. I will post what I find just in case someone else need it.

Thank you,

Basilio.
=)

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.