10.1021/acscentsci.8b00566.s001
Edmund
C. M. Tse
Edmund
C. M.
Tse
Theodore J. Zwang
Theodore J.
Zwang
Sebastian Bedoya
Sebastian
Bedoya
Jacqueline K. Barton
Jacqueline K.
Barton
Effective Distance for DNA-Mediated Charge Transport
between Repair Proteins
American Chemical Society
2019
protein affinity changes
82A
DNA-Mediated Charge Transport
protein binding
repair proteins
ensemble binding affinity
DNA CT
DNA repair glycosylase
DNA repair proteins
DNA charge transport
using DNA charge transport chemistry
1.8 μ m
Endonuclease III
decrease DNA floppiness
support DNA charge transport
4S
3509 base pairs
1.2 μ m
2019-01-11 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Effective_Distance_for_DNA-Mediated_Charge_Transport_between_Repair_Proteins/7577846
The stacked aromatic
base pairs within the DNA double helix facilitate
charge transport down its length in the absence of lesions, mismatches,
and other stacking perturbations. DNA repair proteins containing [4Fe4S]
clusters can take advantage of DNA charge transport (CT) chemistry
to scan the genome for mistakes more efficiently. Here we examine
the effective length over which charge can be transported along DNA
between these repair proteins. We define the effective CT distance
as the length of DNA within which two proteins are able to influence
their ensemble affinity to the DNA duplex via CT. Endonuclease III,
a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated
with DNA duplexes of different lengths (1.5–9 kb), and atomic
force microscopy was used to quantify the binding of proteins to these
duplexes to determine how the relative protein affinity changes with
increasing DNA length. A sharp change in binding slope is observed
at 3509 base pairs, or about 1.2 μm, that supports the existence
of two regimes for protein binding, one within the range for DNA CT,
one outside of the range for CT; DNA CT between the redox proteins
bound to DNA effectively decreases the ensemble binding affinity of
oxidized and reduced proteins to DNA. Utilizing an Endonuclease III
mutant Y82A, which is defective in carrying out DNA CT, shows only
one regime for protein binding. Decreasing the temperature to 4 °C
or including metallointercalators on the duplex, both of which should
enhance base stacking and decrease DNA floppiness, leads to extending
the effective length for DNA charge transport to ∼5300 bp or
1.8 μm. These results thus support DNA charge transport between
repair proteins over kilobase distances. The results furthermore highlight
the ability of DNA repair proteins to search the genome quickly and
efficiently using DNA charge transport chemistry.