Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop

Ellen M. Moody, Philip C. Bevilacqua

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

Many hairpin loops are expanded versions of smaller, stable ones. Herein we investigate the extent to which the energetics and structure of d(cGNAg) hairpin loops will tolerate sequence variation. Changing the closing base pair from CG to GC was found to completely eliminate loop-loop interactions; in contrast, expanding the loop at the 3′-end resulted in similar energetics and nonadditivity parameters as the parent loop, suggesting that loop-loop interactions remain intact and highly coupled upon expansion. Together, these data suggest that the CG closing base pair forms an essential platform upon which a stable d(GNA) hairpin loop can fold and that this loop can undergo 3′-expansion with little effect to its structure or energetics.

Original languageEnglish (US)
Pages (from-to)9570-9577
Number of pages8
JournalJournal of the American Chemical Society
Volume126
Issue number31
DOIs
StatePublished - Aug 11 2004

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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