Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Mechanical conversion of low-affinity Integration Host Factor binding
  sites into high-affinity sites   Although DNA is often bent in vivo, it is unclear how DNA-bending forces
modulate DNA-protein binding affinity. Here, we report how a range of
DNA-bending forces modulates the binding of the Integration Host Factor (IHF)
protein to various DNAs. Using solution fluorimetry and electrophoretic
mobility shift assays, we measured the affinity of IHF for DNAs with different
bending forces and sequence mutations. Bending force was adjusted by varying
the fraction of double-stranded DNA in a circular substrate, or by changing the
overall size of the circle (1). DNA constructs contained a pair of Forster
Resonance Energy Transfer dyes that served as probes for affinity assays, and
read out bending forces measured by optical force sensors (2). Small bending
forces significantly increased binding affinity; this effect saturated beyond
~3 pN. Surprisingly, when DNA sequences that bound IHF only weakly were
mechanically bent by circularization, they bound IHF more tightly than the
linear "high-affinity" binding sequence. These findings demonstrate that small
bending forces can greatly augment binding at sites that deviate from a
protein's consensus binding sequence. Since cellular DNA is subject to
mechanical deformation and condensation, affinities of architectural proteins
determined in vitro using short linear DNAs may not reflect in vivo affinities.

9
The categories of this paper are: nlin
13
The categories of this paper are: quant-ph
27
The categories of this paper are: comp-gas
11
The categories of this paper are: hep-lat
33
The categories of this paper are: plasm-ph
5
The categories of this paper are: gr-qc
34
The categories of this paper are: chem-ph
28
The categories of this paper are: alg-geom
1
The categories of this paper are: cs
12
The categories of this paper are: nucl-th
30
The categories of this paper are: q-alg
3
The categories of this paper are: physics
26
The categories of this paper are: bayes-an
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The categories of this paper are: funct-an
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The categories of this paper are: econ
2
The categories of this paper are: math