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Related Concept Videos

Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
PCR01:32

PCR

Overview

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Related Experiment Video

Updated: Jul 7, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
15:28

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Primer extension.

S J Triezenberg1

  • 1Michigan State University, East Lansing, Michigan, USA.

Current Protocols in Molecular Biology
|February 12, 2008
PubMed
Summary

This protocol maps RNA 5' termini and quantifies RNA levels using primer extension with reverse transcriptase. The method analyzes DNA extension products on sequencing gels for accurate RNA analysis.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Accurate RNA quantification and 5' end mapping are crucial for understanding gene expression.
  • Existing methods may have limitations in sensitivity or resolution.

Purpose of the Study:

  • To present a robust protocol for mapping the 5' terminus of RNA.
  • To establish a method for quantifying specific RNA molecules.

Main Methods:

  • Utilizing end-labeled oligonucleotide primers complementary to the target RNA.
  • Performing primer extension with reverse transcriptase and unlabeled deoxynucleotides.
  • Analyzing the resulting single-stranded DNA products on sequencing gels.

Main Results:

More Related Videos

Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo
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Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo

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Expansion Microscopy: High-Resolution Fluorescent Imaging with a Conventional Microscope
08:53

Expansion Microscopy: High-Resolution Fluorescent Imaging with a Conventional Microscope

Published on: December 19, 2025

Related Experiment Videos

Last Updated: Jul 7, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
15:28

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo
10:51

Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo

Published on: October 31, 2014

Expansion Microscopy: High-Resolution Fluorescent Imaging with a Conventional Microscope
08:53

Expansion Microscopy: High-Resolution Fluorescent Imaging with a Conventional Microscope

Published on: December 19, 2025

  • The length of the extended DNA primer precisely maps the 5' end of the RNA molecule.
  • The yield of the primer extension product directly correlates with the abundance of the target RNA.

    • Conclusions:

    • This primer extension protocol provides a reliable method for both 5' end RNA mapping and quantification.
    • The technique offers a sensitive approach for analyzing RNA levels in molecular biology research.