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 Citations (Scopus)

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

Fingerprint

Base Pairing
DNA

All Science Journal Classification (ASJC) codes

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

Cite this

@article{66ff197bae224fa9b1d9e25757b343be,
title = "Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop",
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.",
author = "Moody, {Ellen M.} and Bevilacqua, {Philip C.}",
year = "2004",
month = "8",
day = "11",
doi = "10.1021/ja048368+",
language = "English (US)",
volume = "126",
pages = "9570--9577",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "31",

}

Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop. / Moody, Ellen M.; Bevilacqua, Philip C.

In: Journal of the American Chemical Society, Vol. 126, No. 31, 11.08.2004, p. 9570-9577.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop

AU - Moody, Ellen M.

AU - Bevilacqua, Philip C.

PY - 2004/8/11

Y1 - 2004/8/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=3042643567&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=3042643567&partnerID=8YFLogxK

U2 - 10.1021/ja048368+

DO - 10.1021/ja048368+

M3 - Article

C2 - 15291560

AN - SCOPUS:3042643567

VL - 126

SP - 9570

EP - 9577

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 31

ER -