Strong sequence patterns in eukaryotic promoter regions: Potential implications for DNA structure

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

1. 1. Analysis of eukaryotic sequences reveals recurring trends in upstream regions. Oligomers composed of (G/C)n and (A/T)m blocks are preferentially flanked by (G/C)2 doublets on their 3' rather than on their 5′ ends, that is (G/C)nä(A/T)m(G/C)2 > (G/C)n+2(A/T)m. 2. 2. These trends are stronger for larger n and smaller m. Additional trends are outlined below. 3. 3. The trends are correlated with DNA structural parameters, in particular with twist and roll angles. 4. 4. Generally, the trends hold if the base pair step joining the 5′ (G/C)2 doublet to the (G/C)n (A/T)m oligomer is not undertwisted and is not strongly rolled into the major groove. 5. 5. Other DNA parameters crucial for DNA-protein interactions are discussed as well.

Original languageEnglish
Pages (from-to)597-607
Number of pages11
JournalInternational Journal of Biochemistry
Volume25
Issue number4
DOIs
StatePublished - Apr 1993

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