Nucleic acid sequence analysis

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Several years ago, the European Molecular Biology Organization published guidelines defining how nucleic acid duplex structures can be examined. The guidelines defined three rotational and three translational parameters between the bases comprising a base pair as well as from one base pair to the next. There are five programs readily distributed in order to perform the calculations. We are releasing a sixth which was created to be able to handle not only the calculations of normal duplexes, but also comparably examine mispaired bases, hoogstein base pairs, looped out bases, a single base adjacent to a base pair, intercalated drugs for which a coordinate frame has been defined, etc.

The nucleic acid structure analysis program is written in Fortran and runs in a UNIX or VMS environment (please specify preference). The program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand. A simple interactive user interface allows for one to specify what file is examined and which parameters to calculate. The program was designed so that the user needs to spend a minimal time reading the documentation in order for the program to run. Full disclosure of the mathematics has been made and published so that the user can readily understand what their parameters mean.

The mathematics are unique for this type of calculation and aviod many of the problems previously encountered. In particular, the calculations are performed by a single rotation not sequential rotations avoiding the use of a midway coordinate frame for rotational parameter calculations. This ensures that the magnitude of the rotational parameters is strand free and direction free. Because a single rotation is used, the equations for each rotational parameter are equivalent, therefore, a 5 degree rotation about the X axis is equivalent to a 5 degree rotation about either the Y or the Z axis. This is not always true of other mathematical formulations presently being used. The mathematics used for calculating the complementary base parameters is identical to the math used to calculate the neighboring base/base pair parameters except that different axes are involved. This is not generally the case of the other available programs. In addition, since the calculations are bases upon local considerations, the value of the parameter depends on only the bases involved and are independent of adjacent bases. This allows for more accurate comparison of parameters from one structure to another.

Copies of the code can be acquired by e-mailing me at:

Marla@Rutchm.Rutgers.edu.

Dr. Marla Babcock

Dept of Chemistry

Rutgers University

P.O. Box 939

Piscataway, N.J. U.S.A 08855

Useful References

A users guide to the programs is provided in the paper:: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: A Users Guide to a Collection of New Analysis Programs," Journal of Biomolecular Structure and Dynamics, Vol. 11, No. 3, pp 597-628, 1993.
The issues surrounding the definition of nucleic acid structure parameters and how we address these issues are discussed in:: Babcock, M.S., and Olson, W.K., "A New Program for the Analysis of Nucleic Acid Structure Interpretation," in Computation of Biomolecular Structures: Achievements, Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M., Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993.
The mathematical definitions of the nucleic acid structure parameters and the methods used to calculate them are presented in:: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That are Truly Comparable Between Structures," Journal of Molecular Biology, Vol. 237, pp 125-156, 1994.
In order to take into account base-stacking effects and other physical constraints, the mathematical definitions we have developed contain parameters called "pivot points", which are the points about which the bases in a structure buckle, propeller twist, and open. The statistical analyses that were performed to determine the optimum positions of the pivot points are presented in:: Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and Coordinate System on Comparability and 'Dependencies' of Nucleic Acid Structure Parameters," Journal of Molecular Biology, Vol. 237, pp 98-125, 1994.

Please send your comments and your suggestions to Yves Epelboin, epelboin@lmcp.jussieu.fr .

Last update Sept. 18/09/1995 Y.E.

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