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The DNA Helix

The DNA Helix

The DNA Helix

The DNA Helix

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...

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.
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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...

The DNA Helix

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

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Related Experiment Video

Updated: Jul 17, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Flexing and folding double helical DNA

W K Olson¹, M S Babcock, A Gorin

¹Department of Chemistry, Rutgers, State University of New Jersey, New Brunswick 08903, USA.

Biophysical Chemistry

|June 1, 1995

Summary

DNA base sequences dictate three-dimensional structures that influence gene activity. Computational models reveal how DNA's double helix flexibility, sequence-dependent bending, and twisting impact its biological functions.

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Area of Science:

Molecular Biology
Biophysics
Computational Chemistry

Background:

DNA base sequence is recognized for its structural role in modulating gene activity.
Nucleic acid sequences define three-dimensional structures with unique properties.
DNA double helix can undergo tertiary folding, albeit gradually and on a larger scale than proteins.

Purpose of the Study:

To understand how local DNA structural irregularities translate to the macromolecular level.
To investigate how DNA structure is recognized by proteins.
To probe the structure and properties of the DNA double helix.

Main Methods:

Utilized a combination of computational techniques.
Incorporated sequence-dependent bending, twisting, and translation of dimeric fragments into computer models.
Developed new base sequence-dependent elastic energy potentials based on B-DNA crystallographic data.

Main Results:

Computer models of open and closed DNA structures were created.
The study monitored the extent to which the double helix can bend and twist.
Sequence-dependent DNA structural properties were quantified.

Conclusions:

DNA base sequence is a critical determinant of its three-dimensional structure and biological function.
Computational modeling provides insights into DNA's mechanical properties and sequence recognition.
Understanding DNA's structural flexibility is key to deciphering its interactions with proteins.