Parallel and antiparallel holliday junctions differ in structure and stability

Min Lu, Qiu Guo, Nadrian Seeman, Neville R. Kallenbach

Research output: Contribution to journalArticle

Abstract

Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy difference between JA and JP using two different methods. One is a direct measurement of the ratio of the equilibrium constants for formation of branched structures from intact duplexes using one labeled strand and a competition assay. The second method estimates the difference in stability from the difference in thermal denaturation temperatures of JA and JP, using urea to shift the tm of the complexes. Both methods reveal a small free energy difference between the two complexes: JA is more stable than JP by -1.1(± 0.4) kcal (mol junction)-1, at 25 °C, 5 mm-Mg2+, from the first method, and by -1.6(± 0.3) kcal (mol junction)-1, according to the second. DNase I and the resolvase, endonuclease I from phage T7, cleave JA differently from JP in the vicinity of the branch, indicating that the structures of these two models differ at this site. Diethyl pyrocarbonate also reveals a difference in the major grooves. Comparison of the scission patterns of JA and JP by the reactive chemical probes methidium-propyl-EDTA · · Fe(II), [MPE · Fe(II)] and Cu(I)-[o-phenanthroline]2, [(OP)2Cu(I)], indicates that in both cases the branch point is a site of enhanced binding for drugs, as it is in the untethered four-arm junction containing the same core sequence at the branch.

Original languageEnglish (US)
Pages (from-to)1419-1432
Number of pages14
JournalJournal of Molecular Biology
Volume221
Issue number4
DOIs
StatePublished - Oct 20 1991

Fingerprint

Cruciform DNA
Deoxyribonuclease I
Diethyl Pyrocarbonate
Bacteriophage T7
Recombinases
Edetic Acid
Oligonucleotides
Urea
Hot Temperature
Binding Sites
Temperature
Pharmaceutical Preparations

Keywords

  • free energy
  • Holliday structure
  • recombination

ASJC Scopus subject areas

  • Virology

Cite this

Parallel and antiparallel holliday junctions differ in structure and stability. / Lu, Min; Guo, Qiu; Seeman, Nadrian; Kallenbach, Neville R.

In: Journal of Molecular Biology, Vol. 221, No. 4, 20.10.1991, p. 1419-1432.

Research output: Contribution to journalArticle

Lu, Min ; Guo, Qiu ; Seeman, Nadrian ; Kallenbach, Neville R. / Parallel and antiparallel holliday junctions differ in structure and stability. In: Journal of Molecular Biology. 1991 ; Vol. 221, No. 4. pp. 1419-1432.
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