Computer programs for nucleic acids studies. Atomic coordinates of helices and their graphic display.

For the purpose of calculation of NMR and other physiocochemical properties of nucleic acids, a computer program in FORTRAN language has been written. This program provides the printout of the Cartesian and cylindrical coordinates of all atoms of a double-stranded helix of nucleic acid in either A, A' or B conformation with any specified base sequence up to 50 nucleotides or longer. In addition, the interatomic distances between any two atoms or distances (with both perpendicular and parallel components) from the centers of the base rings to any atom in the helix can be calculated. This information has been used for the calculation of the ring current effects of the 1H chemical shift of two short helices. Satisfactory agreement has been found in the comparison between the present data and that obtained from model construction and from the table prepared by Arter and Schmidt. The structure of the helix can also be illustrated in graphic form on a Tektronix 4006 CRT terminal. The presentation can be manipulated, such as selection, enlargement, translation and rotation.