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PCR

PCR

DNA Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

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....

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...

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...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Updated: Nov 26, 2025

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Published on: June 25, 2014

Random Amplified Polymorphic DNA (RAPD) and Derived Techniques.

Kantipudi Nirmal Babu¹, Thotten Elampilay Sheeja^2,3, Divakaran Minoo⁴

¹Indian Institute of Spices Research, Kozhikode, Kerala, India. nirmalbabu30@hotmail.com.

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

|December 10, 2020

Summary

This summary is machine-generated.

Random amplified polymorphic DNA (RAPD) is a cost-effective molecular marker technique for analyzing genetic diversity and relationships in plants. Enhanced RAPD methods improve its utility for various genetic applications.

Keywords:

AP-PCR Bulked segregant analysis CAPS Cultivar identification DAF DNA fingerprinting Genetic diversity Genetic fidelity Mapping Population and evolutionary genetics RAHM RAMPO SCAR SRAP

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Area of Science:

Molecular Biology
Genetics
Plant Science

Background:

Understanding molecular genetics is crucial for genome architecture analysis, evolutionary studies, and taxonomy.
Knowledge of genetic variation and relationships is vital for germplasm classification, utilization, and breeding.
Molecular markers are widely used in plant science for fingerprinting, diagnostics, and trait association.

Purpose of the Study:

To review the applications of Random Amplified Polymorphic DNA (RAPD) and its improved techniques in plant genetics.
To highlight the simplicity, cost-effectiveness, and broad genomic coverage of RAPD markers.
To present protocols and applications of RAPD and related methods for genetic diversity, mapping, and varietal identification.

Main Methods:

Focus on Random Amplified Polymorphic DNA (RAPD) as a primary molecular marker technique.
Discuss improvements and related techniques such as AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM.
Emphasis on simple protocols and applications without requiring prior genome knowledge.

Main Results:

RAPD offers a cost-effective and straightforward method for molecular analysis in plant genetics.
Enhanced RAPD techniques address limitations, expanding the utility of this marker system.
These markers are effective for genetic fingerprinting, diversity analysis, mapping, and varietal identification.

Conclusions:

RAPD and its derivatives are valuable tools for dissecting genome architecture and understanding genetic relationships.
The accessibility and versatility of RAPD-based methods make them suitable for various research and breeding applications.
These molecular markers significantly contribute to plant classification, germplasm utilization, and crop improvement.