DNA spatial considerations in the arrangement of G C and A T blocks

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Intensive computations have been carried out on eukaryotic and prokaryotic DNA sequences present in the GenBank database. These calculations were aimed at studying particular sequence patterns. Previously we have observed a trend in the relative positioning of DNA oligomers with respect to each other. Specifically, we have shown that there is a preference for A T stretches to be inserted inside G C blocks, partitioning the latter. This arrangement is preferred over having a longer G C block with an A T stretch next to it. That is ( G C)n( A T)m( G C)2>( G C)n+2( A T)m. Previously we have attributed this preferred pattern to nucleosome packaging of the DNA. Since the average length of the DNA involved in a single nucleosome formation is 200 bp, oligomers were scored in the analysis only if two identical ones occurred within that distance. Since, in addition, the total length of the oligomers studied is n + m + 2 ≤ 7, the counts of the longer oligomers were quite low. Here we have repeated the analysis on the newer, larger database, with that restriction removed. Our new analysis confirms and strengthens the older findings. Moreover, we have carried out DNA structural analysis of these trends, focusing on the twist and roll angular parameters. We have obtained these values from detailed structural computations on the Cray super computer. Some correlations between these values, DNA flexibility and the sequence trends are observed. We suggest that the positioning of the ( A T)m sequence stretch between the two ( G C) blocks affords greater flexibility in the spatial positioning of the G C sequence elements.

Original languageEnglish
Pages (from-to)97-112
Number of pages16
JournalComputers in Biology and Medicine
Issue number1-2
StatePublished - 1992


  • Computer analysis of DNA sequences
  • DNA sequence patterns
  • DNA structure parameters
  • Role of DNA flexibility
  • Sequence structure relationship
  • Spatial positioning of DNA sequence elements


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