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Related Concept Videos

RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...
Small interfering RNAs (siRNA)02:30

Small interfering RNAs (siRNA)

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...

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DNA Vector-based RNA Interference to Study Gene Function in Cancer
13:10

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Published on: June 4, 2012

siRNA Design Software for a Target Gene-Specific RNA Interference.

Yuki Naito1, Kumiko Ui-Tei

  • 1Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo Tokyo, Japan.

Frontiers in Genetics
|June 16, 2012
PubMed
Summary
This summary is machine-generated.

Small interfering RNA (siRNA) can cause unintended gene silencing, known as off-target effects, due to partial complementarity. Our research links off-target effects to thermodynamic stability, offering software to design specific siRNAs for RNA interference therapy.

Keywords:
off-target effectseed regionsiRNAthermodynamic stability

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • RNA interference (RNAi) utilizes small interfering RNA (siRNA) for sequence-specific gene silencing.
  • RNAi is a valuable tool in functional genomics and therapeutic applications.
  • siRNA-mediated gene silencing is generally specific but can affect unintended genes.

Purpose of the Study:

  • To investigate the phenomenon of off-target effects in siRNA-mediated gene silencing.
  • To identify factors influencing siRNA off-target effects.
  • To develop software for designing specific siRNAs with minimized off-target effects for RNAi applications.

Main Methods:

  • Analysis of siRNA-target duplex complementarity, focusing on the seed region.
  • Correlation of thermodynamic stability of siRNA-target interactions with off-target effects.
  • Development and introduction of siRNA design software.

Main Results:

  • Off-target effects are caused by partial complementarity between siRNA and unintended gene targets, primarily in the seed region.
  • The propensity to induce off-target effects strongly correlates with the thermodynamic stability of the siRNA seed-target duplex.
  • Novel software tools for designing specific and functional siRNAs have been developed.

Conclusions:

  • Minimizing off-target effects is critical for accurate target gene function studies and successful RNAi therapeutics.
  • siRNA design must consider thermodynamic stability to ensure target specificity.
  • Publicly available software is introduced to aid in the design of effective and specific siRNAs for RNAi.