Geometry of a branched DNA structure in solution

J. Promisel Cooper, Paul J Hagerman

Research output: Contribution to journalArticlepeer-review

136 Scopus citations


An approximate geometry of a stable, fourway DNA junction has been determined in free solution by applying the technique of transient electric birefringence. The current approach consists of (i) construction of a set of six molecules in which two of the four arms of a synthetic junction are elongated by approximately 9-fold (in each of the six possible two-arm combinations), (ii) determination of the ratios of the longest birefringence decay time of each elongated junctions to the decay time of a linear control molecule, and (iii) comparison of the experimental ratios with corresponding ratios computed as a function of the junction interarm angle. The result is a set of six angles that define the geometry of the junction. In the presence of magnesium ions, the junctions adopts a geometry in which particular pairs of arms approach colinearity. Furthermore, the geometry of the junction is significantly altered in the absence of magnesium, adopting a more uniform structure, although such an effect is not apparent on gels. The application of transient electric birefringence, as described in the current study, should be useful for the characterization of a broad range of tertiary structures in both DNA and RNA.

Original languageEnglish (US)
Pages (from-to)7336-7340
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number19
StatePublished - 1989
Externally publishedYes

ASJC Scopus subject areas

  • General
  • Genetics


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