jp506832u_si_001.pdf (415.11 kB)
SSB Binding to Single-Stranded DNA Probed Using Solid-State Nanopore Sensors
journal contribution
posted on 2014-10-09, 00:00 authored by Deanpen Japrung, Azadeh Bahrami, Achim Nadzeyka, Lloyd Peto, Sven Bauerdick, Joshua B. Edel, Tim AlbrechtSingle-stranded
DNA (ssDNA) binding protein plays an important
role in the DNA replication process in a wide range of organisms.
It binds to ssDNA to prevent premature reannealing and to protect
it from degradation. Current understanding of SSB/ssDNA interaction
points to a complex mechanism, including SSB motion along the DNA
strand. We report on the first characterization of this interaction
at the single-molecule level using solid-state nanopore sensors, namely
without any labeling or surface immobilization. Our results show that
the presence of SSB on the ssDNA can control the speed of nanopore
translocation, presumably due to strong interactions between SSB and
the nanopore surface. This enables nanopore-based detection of ssDNA
fragments as short as 37 nt, which is normally very difficult with
solid-state nanopore sensors, due to constraints in noise and bandwidth.
Notably, this fragment is considerably shorter than the 65 nt binding
motif, typically required for SSB binding at high salt concentrations.
The nonspecificity of SSB binding to ssDNA further suggests that this
approach could be used for fragment sizing of short ssDNA.