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Related Concept Videos

Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

Overview
Mismatch Repair01:36

Mismatch Repair

Overview
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Conservative Site-specific Recombination and Phase Variation02:53

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...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: Jul 6, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis
07:10

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Published on: July 8, 2025

siRNA specificity searching incorporating mismatch tolerance data.

Alistair M Chalk1, Erik L L Sonnhammer

  • 1Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.

Bioinformatics (Oxford, England)
|April 10, 2008
PubMed
Summary

Short interfering RNAs (siRNAs) can cause unintended gene silencing. This study developed new rules and a web server to predict and assess siRNA specificity, minimizing off-target effects in functional genomics research.

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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Related Experiment Videos

Last Updated: Jul 6, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis
07:10

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Published on: July 8, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Short interfering RNAs (siRNAs) are crucial tools in functional genomics for targeted gene knockdown.
  • Ensuring siRNA specificity and avoiding off-target effects remains a significant challenge.
  • Current methods for assessing siRNA specificity are limited, often relying on simple mismatch counts.

Purpose of the Study:

  • To develop improved design rules for predicting off-target effects of siRNAs.
  • To create a user-friendly web server for assessing siRNA specificity.
  • To provide a flexible tool combining multiple methods for evaluating siRNA off-target potential.

Main Methods:

  • Creation of novel design rules based on experimental data for siRNA specificity.
  • Development of a web server integrating these rules with database searching (RefSeq).
  • Implementation of a scoring system to rank potential off-target matches.

Main Results:

  • Established design rules to predict the likelihood of non-specific siRNA effects.
  • Developed a web server that identifies and ranks potential off-target matches.
  • The server utilizes a scoring system derived from experimental specificity studies.

Conclusions:

  • The developed design rules and web server offer a more robust method for assessing siRNA specificity.
  • This tool aids researchers in selecting more specific siRNAs, reducing off-target effects.
  • Improved siRNA specificity enhances the reliability of functional genomics studies.