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Nucleic Acid Structure

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Updated: Jun 25, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Phenomenological partial-specific volumes for G-quadruplex DNAs.

Lance M Hellman¹, David W Rodgers, Michael Gregory Fried

¹Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY 40536-0509, USA.

European Biophysics Journal : EBJ

|February 25, 2009

Summary

This summary is machine-generated.

Accurate partial-specific volume values are crucial for DNA analysis. This study measured these values for G-quadruplex and single-stranded DNA in varying salt conditions, providing essential data for researchers.

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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

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Published on: September 19, 2017

Area of Science:

Biophysical Chemistry
Molecular Biology
Biochemistry

Background:

Accurate partial-specific volume ([Formula: see text]) values are essential for sedimentation velocity and equilibrium analyses of nucleic acids.
Estimating [Formula: see text] for nucleic acids is challenging due to dependencies on base composition, secondary structure, solvation, and buffer ion conditions.

Purpose of the Study:

To determine the apparent isopotential partial-specific volume (/') for G-quadruplex DNAs and a single-stranded DNA.
To investigate the influence of different salt (NaCl and KCl) concentrations on these values.

Main Methods:

Sedimentation equilibrium measurements were performed on two G-quadruplex DNA fragments (22-mer and 27-mer) and one single-stranded DNA (26-mer).
Measurements were conducted in buffers containing NaCl and KCl across a concentration range of 0.09 M to 2.3 M.
Limiting values of /' were extrapolated to zero salt concentration ([salt] = 0 M).

Main Results:

The study reports specific limiting values of /' for each DNA type in both NaCl and KCl buffers.
For example, the 22-mer G-quadruplex in NaCl had a limiting /' of 0.525 +/- 0.004 mL/g, while in KCl it was 0.531 +/- 0.006 mL/g.
Small variations in /' with salt concentration suggest limited changes in counterion association or hydration.

Conclusions:

The determined partial-specific volume values provide critical data for accurate biophysical characterization of DNA structures.
The findings indicate that salt concentration has a minor effect on the partial-specific volume of these DNA molecules within the tested range.
This research contributes to a better understanding of DNA behavior in solution, aiding in the interpretation of sedimentation analyses.