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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 Central Dogma

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

RACE - Rapid Amplification of cDNA Ends

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Rolling Circle Amplification with an Expanded Genetic Alphabet (ExRCA) Generates DNA Materials Incorporating

Leli Peng¹, Fangkai Ye¹, Ruimin Zhang¹

¹MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China.

Journal of the American Chemical Society

|August 27, 2025

Summary

This summary is machine-generated.

This study introduces expanded genetic alphabet rolling circle amplification (ExRCA), a novel method for efficiently amplifying DNA with unnatural base pairs (UBPs). ExRCA enables new DNA materials and biotechnological applications with enhanced information capacity.

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Area of Science:

Biochemistry
Synthetic Biology
Materials Science

Background:

Unnatural base pairs (UBPs) expand DNA's information capacity and functional diversity.
Efficient amplification methods are critical for the widespread application of UBPs.
Rolling circle amplification (RCA) is a key DNA amplification technique in biotechnology and nanotechnology.

Purpose of the Study:

To evaluate the efficiency and fidelity of phi29 DNA polymerase for replicating UBPs.
To establish an expanded genetic alphabet rolling circle amplification (ExRCA) method.
To demonstrate ExRCA's utility in DNA materials science and biotechnology.

Main Methods:

Replication of unnatural base pairs (UBPs) using phi29 DNA polymerase.
Development of ExRCA for amplifying DNA containing UBPs.
Preparation of circular DNA templates for ExRCA.
Application of ExRCA for producing single- and double-stranded DNA with UBPs.

Main Results:

Phi29 DNA polymerase exhibits high efficiency and fidelity in replicating UBPs like dNaM-dTPT3.
ExRCA was successfully established and demonstrated for amplifying DNA with UBPs.
ExRCA facilitated the synthesis of DNA nanostructures, including DNA tetrahedra.
ExRCA enabled the development of ultrasensitive biosensors, DNA hydrogels, and functional DNA materials.

Conclusions:

ExRCA provides an efficient isothermal amplification method for DNA containing unnatural nucleobases.
UBPs, with natural-like replication efficiency, are valuable for creating advanced DNA materials.
This work expands the potential of synthetic biology and DNA nanotechnology through enhanced genetic information systems.