The following two programs were designed and used for structural interpretation of multimerization-cyclization of short DNA fragments containing bends or unusual motifs. The interpretation procedure is described in details in the following publication:

Podtelezhnikov, A. A.; C. Mao; N. C. Seeman and A. V. Vologodskii. (2000) Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys. J. 79(5)

There are two steps in the procedure. At the first step one should extract j-factors from from the distribution of linear and circular products in a singe reaction of ligation. At the second step one should find the structural parameters that correspond to the extracted j-factors.

The first program, js4.c, extracts the j-factors from the distribution of products. The program is based on numerical solution of kinetic differential equations where the j-factors appear as coefficients. It uses successive approximations of the j-factors. The computations should not take more than a few minutes even on a relatively slow computer. This short program is written in plain C and should be compiled without any problem with any ANSI compliant compiler (for example, for SGI: cc -O js4.c -o js4). This is a command line application, which uses the name of a data file as an argument, i.e., it should be run as follows:

prompt> js4 js4.data

The data file, e.g. js4.data, should contain the following necessary information:

  1. the initial concentration on the monomers in moles per liter;
  2. the final fractional quantities of linear and circular products, which have to be normalized to 1;
  3. whether the sticky ends of the monomer are identical or not.

The example data file, js4.data, contains additional comments.

The output contains the found j-factors in moles per liter. The program also computes the distribution of products corresponding to the found j-factor. Thus, reliability of the computations should be assessed by comparison of the given and computed distributions in the resulting output.

The second program, jfm2.c, was used to calculate the j-factor for a multimer of identical short DNA fragments. Such multimers are products of multimerization-cyclization reaction. This is also a C-program (compile using cc -O jfm2.c -lm -o jfm2), which uses the name of a data file as an argument:

prompt> jfm2 jfm2.data

The data file, e.g. jfm2.data, should contain the following necessary information:

  1. how many monomers are combined in the multimer;
  2. the length of the monomer;
  3. the angle of static bend of the monomer;
  4. the persistence length of DNA;
  5. the helical repeat;
  6. the torsional rigidity of the monomer.

The example data file, jfm2.data, contains additional comments.

The output is the j-factor and the standard error of its determination in moles per liter. The program uses an efficient algorithm and calculates series of partial probabilities. The normal course of calculations should not take more than 1 hour.