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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. ...

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 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...

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...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Related Experiment Video

Updated: Mar 25, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases.

Sandra Sagredo¹, Tobias Pirzer², Ali Aghebat Rafat²

¹Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Albert Einstein 22, 39011, Santander, Spain.

Angewandte Chemie (International Ed. in English)

|February 27, 2016

Summary

Relaxase proteins offer precise DNA nanostructure modification. These DNA-binding proteins demonstrate orthogonal binding, making them valuable for advanced nanofunctionalization applications.

Keywords:

DNA nanotechnology DNA origami bacterial conjugation bioconjugation relaxase

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Last Updated: Mar 25, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack

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Published on: August 15, 2018

Assembly of Gold Nanorods into Chiral Plasmonic Metamolecules Using DNA Origami Templates

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Published on: March 5, 2019

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Area of Science:

Biochemistry
Nanotechnology
Molecular Biology

Background:

DNA-binding proteins are key for modifying DNA nanostructures.
Relaxases, involved in bacterial plasmid transfer, bind DNA via a covalent linkage.

Purpose of the Study:

To evaluate relaxase proteins (TrwC, TraI, MobA) for DNA nanostructure functionalization.
To assess the binding specificity and efficiency of relaxases on DNA origami.

Main Methods:

Investigated relaxase binding to rodlike six-helix bundle and flat rectangular DNA origami structures.
Quantified binding yields and assessed orthogonality of protein-DNA interactions.

Main Results:

Achieved highly orthogonal binding of relaxases to DNA nanostructures, with yields of 40-50% per site.
Observed variations in binding yields based on origami structure and binding site location.
Demonstrated relaxases' specificity for single-stranded DNA targets.

Conclusions:

Relaxase proteins are effective and orthogonal tools for DNA nanostructure modification.
Their unique binding properties expand the capabilities for protein-DNA nanotechnology.
Relaxases represent a valuable addition to the protein engineering toolbox for nanostructures.