Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Southern Blot

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Electroelution Into a Salt Trap: Reviving an Old-School Approach to DNA Purification.

Small methods·2026

Same author

Genetic Diversity of <i>Rhodiola quadrifida</i> (Crassulaceae) in Altai High-Mountain Populations of Kazakhstan.

Genes·2025

Same author

Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats.

Bioinformatics and biology insights·2024

Same author

Identification of SNPs Associated with Drought Resistance in Hybrid Populations of <i>Picea abies</i> (L.) H. Karst.-<i>P. obovata</i> (Ledeb.).

Genes·2024

Same author

Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of <i>Pinus sylvestris</i> L. Populations in the Urals.

Genes·2024

Same author

The Proteolytic Activity of Neutrophil-Derived Serine Proteases Bound to the Cell Surface Arming Lung Epithelial Cells for Viral Defense.

Molecules (Basel, Switzerland)·2024

Search research articles

Related Experiment Video

Updated: May 4, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

An Assay for Variable Fragment Length Allele-Specific Genotyping.

Ruslan Kalendar¹, Vladislav Shevtsov², Aisulu Ismailova²

¹National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan. ruslan.kalendar@helsinki.fi.

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

|June 28, 2025

Summary

Allele-specific PCR enables precise detection of genetic variations using bioinformatics tools. This method designs multiplexed primer assays for accurate genotyping of single-nucleotide polymorphisms and insertions/deletions.

Keywords:

Genotyping assay design software Genotyping system Insertion-deletion polymorphism (InDel)Multiplex Multiplex Ligation-dependent Probe Amplification (MLPA)SNaPshot Single-nucleotide polymorphism (SNP)

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Published on: September 16, 2019

Related Experiment Videos

Last Updated: May 4, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Published on: September 16, 2019

Area of Science:

Molecular Biology
Bioinformatics
Genetics

Background:

Polymerase chain reaction (PCR) is a fundamental technique for detecting nucleotide polymorphisms and sequence variations.
Allele-specific PCR (AS-PCR) employs competitive reactions with allele-specific primers to amplify targeted alleles.
Existing methods require robust tools for designing accurate genotyping assays.

Purpose of the Study:

To present protocols for a bioinformatics tool designed for creating PCR-based genotyping assays.
To enable the design of variable fragment length allele-specific genotyping assays.
To provide a guide for developing multiplexed primer assays for genetic variation detection.

Main Methods:

Utilizing a bioinformatics tool for designing allele-specific PCR assays.
Developing assays capable of targeting both single-nucleotide polymorphisms (SNPs) and insertion/deletions (indels).
Designing assays in both forward and reverse directions for comprehensive genotyping.

Main Results:

Successful design of PCR-based genotyping assays for variable fragment length allele-specific genotyping.
Demonstration of the tool's capability to handle both SNPs and indels.
Establishment of a protocol for creating multiplexed primer sets for high-throughput genotyping.

Conclusions:

The presented bioinformatics tool facilitates the design of efficient allele-specific PCR genotyping assays.
The developed method supports the accurate identification of various genetic variations.
This approach enhances the application of PCR in genetic research, diagnostics, and agriculture.