Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch

Q. Guo, M. Lu, N. R. Kallenbach

Research output: Contribution to journalArticle

Abstract

Four-arm DNA branched junctions are stable analogues of Holliday recombinational intermediates. A number of four-arm DNA junctions synthesized from oligonucleotides have now been studied. Gel mobility or chemical footprinting experiments on several immobile four-arm junctions indicate that in the presence of Mg2+, they assume a preferred conformation consisting of two helical domains, each formed by stacking a particular pair of arms on each other. We show here that a junction we designate as J1(c) that has the same chemical composition as one we have previously studied in detail, J1, but is formed from the four strands complementary to those of the latter, exhibits the reverse stacking preference. The pattern of self-protection of the strands of J1(c) exposed to Fe(II) · EDTA-induced scission reveals that twofold symmetry is preserved, but the opposite pair of strands preferentially cross over. Moreover, the Fe(II) · EDTA scission profiles of J1(c) indicate that this junction exhibits a weaker bias as to which strands cross over than is observed in J1. The preference for the dominant species in J1 is 1.3 times greater than in J1(c) at 4°C and in the presence of 10 mM Mg2+, based on chemical reactivity data. This is confirmed by a cleavage experiment using the resolvase enzyme, endonuclease I, from bacteriophage T7. This difference could reflect either sequence-dependent differences in the equilibrium among isomers, or in the structure of these junctions. Chemical footprinting experiments using the probes MPE·Fe(II) and (OP)2Cu(I) show that the high-affinity ligand binding site in immobile junctions is determined by junction geometry.

Original languageEnglish (US)
Pages (from-to)359-372
Number of pages14
JournalBiopolymers - Peptide Science Section
Volume31
Issue number4
StatePublished - Mar 1991

Fingerprint

DNA
Ligands
Ethylenediaminetetraacetic acid
Bacteriophage T7
Recombinases
Deoxyribonuclease I
Oligonucleotides
Chemical reactivity
Bacteriophages
Gels
Experiments
Binding Sites
Binding sites
Isomers
Conformations
Enzymes
Geometry
Chemical analysis
Fe(II)-EDTA
1,10-phenanthroline

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch. / Guo, Q.; Lu, M.; Kallenbach, N. R.

In: Biopolymers - Peptide Science Section, Vol. 31, No. 4, 03.1991, p. 359-372.

Research output: Contribution to journalArticle

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