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© 1988 IRL Press Ltd

The translation of DNA primary base sequence into three-dimensional structure

Wilma K. Olson * and A. R. Srinivasan

Department of Chemistry, Rutgers, The State University New Brunswick, NJ 08903, USA

*To whom reprint requests should be sent

A procedure is outlined to obtain a reliable computer-generated representation of the DNA duplex from its primary sequence of base pairs. The calculations are based on the potential energies of interaction of adjacent side groups. The methods are, however, completely general and can be adapted to any set of base sequence dependent conformational rules. Static representations of the DNA are compared with the distributions of conformations obtained from Monte Carlo simulation studies. Direct matrix generator calculations of the average (equilibrium) extension and orientation of various sequences and numerical estimates of the flexibility of the chains as a whole are also reported. The methods are applied to three short fragments of kinetoplast DNA from Crithidia fasciculata which exhibit dramatically different behavior on non-denaturing poly-acrylamide gels.

Received on August 17, 1987; accepted on December 19, 1987

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