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DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

DNA Topoisomerases

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...

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...

DNA Helicases

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...

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...

The DNA Replication Fork

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...

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Related Experiment Video

Updated: Jun 10, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Sequence dependence of DNA bending rigidity.

Stephanie Geggier¹, Alexander Vologodskii

¹Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003, USA.

Proceedings of the National Academy of Sciences of the United States of America

|August 13, 2010

Summary

This study quantifies DNA bending rigidity based on DNA sequence. Researchers accurately determined DNA persistence length (a) for dinucleotide steps, resolving a long-standing problem in DNA-protein interactions.

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Area of Science:

Molecular Biology
Biophysics
Genetics

Background:

DNA bending rigidity, or persistence length (a), is crucial for understanding DNA-protein interactions.
Sequence-dependent variations in DNA flexibility remain a significant challenge in molecular biology.

Purpose of the Study:

To accurately determine the sequence-specific DNA bending rigidity (persistence length, a).
To establish a quantitative relationship between DNA sequence and its flexibility.

Main Methods:

Utilized a DNA cyclization assay to precisely measure persistence length (a).
Assigned specific persistence length (a) values to 10 distinct dinucleotide steps.
Analyzed cyclization efficiencies (j factors) of ~200 bp DNA fragments with quasi-periodic sequences.

Main Results:

Developed a comprehensive set of persistence length (a) values for all dinucleotide steps.
Experimental validation confirmed the accuracy of calculated persistence length (a) values.
Revealed sequence-dependent variations in DNA helical repeat.

Conclusions:

Successfully determined the sequence dependence of DNA bending rigidity (persistence length, a).
The findings provide a foundational tool for predicting DNA flexibility based on sequence.
This work resolves a long-standing problem in understanding DNA structure-function relationships.