Thermodynamics of forming a parallel DNA crossover

Charles H. Spink, Liang Ding, Qingyi Yang, Richard D. Sheardy, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

The process of genetic recombination involves the formation of branched four-stranded DNA structures known as Holliday junctions. The Holliday junction is known to have an antiparallel orientation of its helices, i.e., the crossover occurs between strands of opposite polarity. Some intermediates in this process are known to involve two crossover sites, and these may involve crossovers between strands of identical polarity. Surprisingly, if a crossover occurs at every possible juxtaposition of backbones between parallel DNA double helices, the molecules form a paranemic structure with two helical domains, known as PX-DNA. Model PX-DNA molecules can be constructed from a variety of DNA molecules with five nucleotide pairs in the minor groove and six, seven or eight nucleotide pairs in the major groove. A topoisomer of the PX motif is the juxtaposed JX1 molecule, wherein one crossover is missing between the two helical domains. The JX1 molecule offers an outstanding baseline molecule with which to compare the PX molecule, so as to measure the thermodynamic cost of forming a crossover in a parallel molecule. We have made these measurements using calorimetric and ultraviolet hypochromicity methods, as well as denaturing gradient gel electrophoretic methods. The results suggest that in relaxed conditions, a system that meets the pairing requirements for PX-DNA would prefer to form the PX motif relative to juxtaposed molecules, particularly for the 6:5 structure.

Original languageEnglish (US)
Pages (from-to)528-538
Number of pages11
JournalBiophysical Journal
Volume97
Issue number2
DOIs
StatePublished - 2009

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Thermodynamics
DNA
Cruciform DNA
Nucleotides
Genetic Recombination
Gels
Costs and Cost Analysis

ASJC Scopus subject areas

  • Biophysics

Cite this

Thermodynamics of forming a parallel DNA crossover. / Spink, Charles H.; Ding, Liang; Yang, Qingyi; Sheardy, Richard D.; Seeman, Nadrian.

In: Biophysical Journal, Vol. 97, No. 2, 2009, p. 528-538.

Research output: Contribution to journalArticle

Spink, CH, Ding, L, Yang, Q, Sheardy, RD & Seeman, N 2009, 'Thermodynamics of forming a parallel DNA crossover', Biophysical Journal, vol. 97, no. 2, pp. 528-538. https://doi.org/10.1016/j.bpj.2009.04.054
Spink, Charles H. ; Ding, Liang ; Yang, Qingyi ; Sheardy, Richard D. ; Seeman, Nadrian. / Thermodynamics of forming a parallel DNA crossover. In: Biophysical Journal. 2009 ; Vol. 97, No. 2. pp. 528-538.
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