J. Biol. Chem., Vol. 265, Issue 28, 16778-16785, Oct, 1990
Characterization of a bimobile DNA junction
M Lu, Q Guo, JE Mueller, B Kemper, FW Studier, NC Seeman and NR Kallenbach
Department of Chemistry, New York University, New York 10003.
We present here a chemical and enzymatic footprinting analysis of a
branched DNA molecule formed from four complementary 50-mer strands. These
strands are designed to form a stable junction, in which two steps of
branch point migration freedom are possible. Exposure of the junction to
Fe(II).EDTA shows protection of 3 or 4 residues in each strand at the
branch, while two resolvase enzymes (endonuclease VII from phage T4 and
endonuclease I from phage T7), cleave all four strand near the branch.
Chemical footprinting of this junction using the reagents MPE.Fe(II) and
(OP)2Cu(I) shows that the branch site is hyper- reactive to cutting induced
by these probes as it is in an immobile four-arm junction. The effects
involve more residues than in the immobile case. In the absence of divalent
cations, the structure of the junction alters, sites of enhanced cleavage
by MPE.Fe(II) and (OP)2Cu(I) disappear, and purines at the branch become
reactive to diethyl pyrocarbonate. Our interpretation of these results is
based on the properties of immobile junction analogs and their response to
these probes. In the presence of Mg2+, the three migrational isomers
coexist, each probably in the form of a 2-fold symmetric structure with two
helical arms stacked.
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