Introduction
The bending of DNA strands is a common
phenomenon either intrinsic or induced
by protein binding and/or other changes
in the physiological environment (such
as local ion concentrations). It is believed
to play an important role in the control of
gene expression, replication, recombination,
and packaging in the nucleus. Kinking,
roughly defined as abrupt bending, is a
distinct category of DNA bending and is
often observed in protein-DNA complexes.
Numerous methods are available to detect
structural fluctuations in DNA. To clearly
distinguish between smoothly distributed
bending and highly localized kinking, however,
a spatial resolution on the order of at least
1 nm is required.
Among many high-resolution imaging tools,
the atomic force microscope (AFM), with
easy sample preparation and close to native
imaging conditions, stands out as one of
the best options for biologists. Its near-
atomic resolution makes it useful for in situ
imaging of conformational changes in DNA
molecules. Due to tip-broadening effects,
however, the width of DNA molecules
obtained with atomic force microscopy has
been on the order of 5 nm.