3DNA logo A Software Package for the Analysis, Rebuilding, and Visualization of Three-dimensional Nucleic Acid Structures
Xiang-Jun Lu & Wilma K. Olson

3DNA was created in the hope that it will be useful, but without any guarantees. Nothing is perfect, and we strive to improve its functionalities. Any comments, constructive suggestions, and bug reports are welcome.
 

Background information on the calculation of nucleic acid structural parameters

  • Nomenclature: The 1989 EMBO Workshop held at Cambridge, England, provided the "definitions and nomenclature of nucleic acid structure parameters" (Dickerson et al. (1989), J. Mol. Biol., 208, 787-791). Following that, several analysis programs were modified or created (e.g., Curves, NewHelix/FreeHelix, etc.). All claimed to follow the loosely defined convention. Even though the same parameters (e.g., Slide, Rise) were calculated by the different programs, it was well-known in the community that they gave conflicting numerical values, especially for strongly distorted structures.
  • Reference Frame: Our result (Lu & Olson (1999), J. Mol. Biol. 285(4), 1563-1575) demonstrated that 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.

    To resolve the numerical discrepancies, the 1999 Tsukuba Workshop on nucleic acid structure and interactions recommended "a standard reference frame for the description of nucleic acid base-pair geometry" (Olson et al. (2001), J. Mol. Biol. 313(1), 229-237). This base-centered standard reference frame follows most closely those used originally in Curves and CompDNA.

    The numerical values calculated by 3DNA conform to this new reference frame. For back-reference, authentic parameters based on the programs CEHS and RNA are also available.
  • Standard Method: To eliminate any last possible discrepancies, Dr. Ramswamy H. Sarma organized a Workshop at the 13th Conversation at Albany, NY, in June 2003. The program was coordinated by Dr. Thomas E. Cheatham, III. Even though no final agreement was reached, the lively discussions in the email list before the Workshop provided interesting insights into unresolved issues.

    The electronic debate is presented below:
    1. Dr. Sarma's initial call for the Workshop (April 16)
    2. Proposal of Dr. Heinz Sklenar (May 06)
    3. Dr. Olson's follow-up regarding 3DNA manuscript (May 19)
    4. Dr. Sklenar's view on mean-frame definition (June 01)
    5. Dr. Sklenar's revision on mean-frame definition and order of rotation (June 05)
    6. Dr. Olson's and Dr. Victor Zhurkin's follow-up and proposal (June 05)
    7. Dr. Lu's follow-up (June 06)
    8. Dr. Sklenar's response (June 08)
    9. Dr. Lu's follow-up (June 09)
    10. Dr. Cheatham's summary (June 09)
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