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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...

Proofreading

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...

Proofreading

Proofreading

The Replisome

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...

The Replisome

The Replisome

Replication in Eukaryotes

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Related Experiment Video

Updated: Dec 4, 2025

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

Published on: October 6, 2017

DNA polymerase β: Closing the gap between structure and function.

William A Beard¹

¹Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA.

|October 22, 2020

Summary

This summary is machine-generated.

DNA polymerase beta (dpol β) fidelity relies on efficient correct nucleotide insertion, not just poor incorrect insertion. Computational and structural methods reveal molecular details of this DNA synthesis selectivity.

Keywords:

DNA polymerase β DNA synthesis Fidelity Genome integrity Structure

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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

DNA polymerase beta (dpol β) is a model enzyme for DNA synthesis.
Understanding enzyme selectivity in nucleotide insertion is crucial for DNA replication and repair.

Purpose of the Study:

To explore the molecular mechanisms underlying DNA polymerase beta's fidelity.
To bridge the gap between static structures and dynamic kinetic processes in DNA synthesis.

Main Methods:

Multifunctional approach integrating structural biology (crystallography), kinetics, spectroscopy, and computational modeling.
Analysis of dpol β in various liganded states.

Main Results:

Correlating static enzyme structures with kinetic data is challenging.
Novel insights into nucleotide insertion selectivity were gained using computational and spectroscopic methods.
Enzyme's ability to select the correct nucleotide is determined by the efficiency of inserting the right one.

Conclusions:

DNA polymerase fidelity is governed by the efficiency of correct nucleotide insertion.
Molecular attributes of dpol β facilitate correct insertion and hinder incorrect insertion.
Computational approaches are vital for understanding the dynamics of DNA synthesis and enzyme-ligand interactions.