Conformational transitions of synthetic DNA sequences with inserted bases, related to the dodecamer d(CGCGAATTCGCG)

Maria Miller, William Kirchhoff, Frederick Schwarz, Ettore Appella, Yuan Yuan H. Chiu, Jack S. Cohen, Joel L. Sussman

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Conformational transitions for a series of imperfect palindromes related to the dodecamer d(CGCGAATTCGCG) have been investigated. These sequences are: two isomeric 13-mers - d(CGCGAATTCGCG) (13-merI) and d(CGCGAATTACGCG) (13-merII), 17-mer d(CGCGCGAATTACGCGCG) and 15-mer d(CGCGAAATTTACGCG). Insertion of a single adenine nucleotide prevents these sequences from being self-complementary. Analysis of thermodynamic parameters derived from the melting profiles together with other data at higher concentrations (NMR and calorimetry) indicates that the insertion of the additional nucleotide which lacks a complement in the opposite strand does not change the enthalpy of the duplex formation, but does alter the number of stable nucleation configurations. The relative position of the insertion within the self-complementary sequence determines the equilibrium between the duplex form and the single-stranded hairpin loop. C-G segments separated by the insertion from the rest of the molecule can undergo an independent conformational transition at high salt concentration, probably to the Z form.

Original languageEnglish
Pages (from-to)3877-3890
Number of pages14
JournalNucleic Acids Research
Volume15
Issue number9
DOIs
StatePublished - 11 May 1987
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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