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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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An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

Published on: November 29, 2016

A simple model for exploring conformation of highly-charged electrosprayed single-stranded oligonucleotides.

David Touboul¹, Renato Zenobi

¹Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland.

Chemical Communications (Cambridge, England)

|February 12, 2009

Summary

Single-stranded polynucleotides adopt compact shapes in positive ion mode electrospray and linear structures in negative ion mode. This finding impacts understanding of biomolecule conformation and analysis.

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Chemical Triphosphorylation of Oligonucleotides

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Published on: June 2, 2022

Area of Science:

Biochemistry
Analytical Chemistry
Physical Chemistry

Background:

Electrospray ionization is a key technique for analyzing biomolecules.
Understanding the conformation of single-stranded polynucleotides is crucial for their characterization.

Purpose of the Study:

To investigate the relationship between molecular weight and maximum charge state of single-stranded polynucleotides.
To determine the influence of ion mode on the conformation of these molecules during electrospray analysis.

Main Methods:

Analysis of single-stranded polynucleotides using electrospray.
Measurement of maximum charge state as a function of molecular weight.
Comparison of conformations in positive and negative ion modes.

Main Results:

A correlation was observed between molecular weight and maximum charge state.
Single-stranded polynucleotides exhibit compact conformations in positive ion mode.
Linear structures are predominant for these molecules in negative ion mode.

Conclusions:

The ion mode significantly influences the observed conformation of single-stranded polynucleotides.
Electrospray analysis provides insights into the structural behavior of biomolecules based on charge state and ion polarity.