We have used atomic force microscopy (AFM) to study the conformation of thr
ee-way DNA junctions, intermediates of DNA replication and recombination, I
mmobile three-way junctions with one hairpin arm (50, 27, 18 and 7 bp long)
and two relatively long linear arms were obtained by annealing two partial
ly homologous restriction fragments. Fragments containing inverted repeats
of specific length formed hairpins after denaturation, Three-way junctions
were Obtained by annealing one strand of a fragment from:a parental plasmid
with one strand of an inverted repeat-containing fragment, purified from g
els, and examined by AFM, The molecules are clearly seen as three-armed mol
ecules with one short aim and two flexible long arms, The AFM analysis reve
aled two important features of three-way DNA junctions, First, three-way ju
nctions are very dynamic structures. This conclusion is supported by a high
variability of the inter-arm angle detected on dried samples. The mobility
of the junctions was observed directly by imaging the samples in liquid (A
FM;in situ), Second, measurements of the angle between the arms led to the
conclusion that three-way junctions are not flat, but rather pyramid-like,
Non-flatness of the junction should be taken into account in analysis of th
e AFM data.