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Single-Strand DNA Binding Proteins

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores

Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores

Published on: October 31, 2013

Unraveling single-stranded DNA in a solid-state nanopore.

Stefan W Kowalczyk¹, Maarten W Tuijtel, Serge P Donkers

¹Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.

|March 19, 2010

Summary

Single-stranded DNA (ssDNA) forms large, entangled coils that must unravel for nanopore translocation. This process shows voltage-dependent translocation times distinct from double-stranded DNA (dsDNA).

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Area of Science:

Nanotechnology
Biophysics
Molecular Biology

Background:

Solid-state nanopores are advanced single-molecule sensors.
Research has primarily focused on double-stranded DNA (dsDNA) translocation.
Single-stranded DNA (ssDNA) analysis is crucial for applications like DNA sequencing.

Purpose of the Study:

Investigate the translocation dynamics of long, random-sequence ssDNA through solid-state nanopores.
Characterize the behavior of ssDNA structures at the nanopore entrance.
Compare ssDNA translocation with dsDNA using conductance-blockade levels and voltage dependence.

Main Methods:

Atomic Force Microscopy (AFM) to visualize ssDNA hybridization and structure.
Solid-state nanopore experiments to measure ssDNA translocation events.
Electrical measurements to determine conductance-blockade levels and translocation times.

Main Results:

ssDNA forms random coils (approx. 100 nm diameter for 7 kb ssDNA) that entangle.
Translocation blockade events are observed for ssDNA.
ssDNA translocation time exhibits exponential voltage dependence (τ ∝ e^(-V/V₀)), differing from dsDNA (τ ∝ 1/V).
Comparative analysis of conductance-blockade for ssDNA and dsDNA constructs as a function of voltage.

Conclusions:

The unravelling of entangled ssDNA structures significantly influences translocation dynamics.
The distinct voltage dependence of ssDNA translocation provides insights into its behavior in nanopores.
Understanding ssDNA translocation is key for developing advanced nanopore-based sequencing technologies.