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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...

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...

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.
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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...

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.
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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.
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Related Experiment Video

Updated: Jul 30, 2025

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

Parallel Functionalization of DNA Origami.

Rasmus P Thomsen¹, Rasmus S Sørensen¹, Jørgen Kjems²

¹Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.

Methods in Molecular Biology (Clifton, N.J.)

|May 11, 2023

Summary

This study presents a novel method for creating diverse nanoscale patterns using DNA origami. The technique employs enzymatic functionalization of staple strands, offering flexibility, cost-effectiveness, and speed for molecular patterning applications.

Keywords:

DNA DNA origami Enzymatic Functionalization Nanotechnology

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Last Updated: Jul 30, 2025

Folding and Characterization of a Bio-responsive Robot from DNA Origami

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Designing a Bio-responsive Robot from DNA Origami

Designing a Bio-responsive Robot from DNA Origami

Published on: July 8, 2013

Area of Science:

Nanotechnology
Biochemistry
Molecular Biology

Background:

DNA origami allows for the construction of nanoscale structures with precise features.
Existing methods for nanoscale patterning often require custom oligonucleotides for each unique pattern, which can be costly and time-consuming.

Purpose of the Study:

To present a method for creating diverse nanoscale patterns on DNA origami canvases.
To demonstrate the use of enzymatic functionalization for flexible and cost-effective molecular patterning.

Main Methods:

Utilizing the enzyme terminal deoxynucleotidyl transferase (TdT) for parallelized functionalization of staple strands.
Incorporating modified staple strands into DNA origami structures at defined positions.
Synthesizing functionalized oligonucleotides in a one-pot reaction without individual post-purification.

Main Results:

Achieved high flexibility and versatility in creating various molecular patterns and arrays.
Demonstrated cost-effectiveness and speed compared to custom synthesis, especially for small-scale applications.
Successfully incorporated diverse molecules, including proteins and modified nucleotide triphosphate (NTP) building blocks.

Conclusions:

Enzymatic functionalization of DNA origami staple strands provides an efficient and adaptable approach to nanoscale molecular patterning.
This method facilitates rapid screening of molecular patterns and reduces synthesis costs.
The technique enables the creation of complex, designed functionalities on DNA origami scaffolds.