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

Wilma Olson, A. R. Srinivasan

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)133-142
Number of pages10
JournalBioinformatics
Volume4
Issue number1
DOIs
StatePublished - Mar 1 1988

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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