Measuring
the mechanical properties of single-stranded DNA (ssDNA)
is a challenge that has been addressed by different methods lately.
The short persistence length, fragile structure, and the appearance
of stem loops complicate the measurement, and this leads to a large
variability in the measured values. Here we describe an innovative
method based on DNA origami for studying the biophysical properties
of ssDNA. By synthesizing a DNA origami structure that consists of
two rigid rods with an ssDNA segment between them, we developed a
method to characterize the effective persistence length of a random-sequence
ssDNA while allowing the formation of stem loops. We imaged the structure
with an atomic force microscope (AFM); the rigid rods provide a means
for the exact identification of the ssDNA ends. This leads to an accurate
determination of the end-to-end distance of each ssDNA segment, and
by fitting the measured distribution to the ideal chain polymer model
we measured an effective persistence length of 1.98 ± 0.72 nm.
This method enables one to measure short or long strands of ssDNA,
and it can cope with the formation of stem loops that are often formed
along ssDNA. We envision that this method can be used for measuring
stem loops for determining the effect of repetitive nucleotide sequences
and environmental conditions on the mechanical properties of ssDNA
and the effect of interacting proteins with ssDNA. We further noted
that the method can be extended to nanoprobes for measuring the interactions
of specific DNA sequences, because the DNA origami rods (or similar
structures) can hold multiple fluorescent probes that can be easily
detected.
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