Related Experiment Video
Updated: Jul 14, 2026
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
A structure-activity relationship study of siRNAs with structural variations.
Chan Il Chang1, Sun Woo Hong, Soyoun Kim
1Department of Chemistry and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea.
Biochemical and Biophysical Research Communications
|June 20, 2007
Summary
This study explores how structural changes in small interfering RNAs (siRNAs) affect gene silencing. Some modified siRNAs work well, while others lose effectiveness, impacting RNA-based therapies.
Area of Science:
- Molecular Biology
- RNA Interference
- Gene Silencing
Background:
- Small interfering RNAs (siRNAs) are key for targeted gene knockdown in mammalian cells.
- Variations in siRNA structure, including longer forms and incorporated modules, aim to enhance silencing efficiency.
- The impact of these structural modifications on siRNA activity remains incompletely understood.
Purpose of the Study:
- To conduct a systematic structure-activity relationship study of siRNA variants.
- To investigate the effect of attaching non-target sequences on conventional siRNA structures.
- To evaluate silencing efficiency, off-target effects, and innate immune responses of modified siRNAs.
Main Methods:
- Synthesis and characterization of various siRNA structural variants.
- Assessment of gene silencing efficiency in mammalian cells.
- Measurement of off-target effects and innate immune responses.
- In vitro Dicer cleavage assays to analyze substrate processing.
Main Results:
- SiRNA structural variants exhibited differential silencing efficiencies, with some showing reduced or absent activity.
- All tested variants were Dicer substrates, but digestion patterns varied significantly.
- Off-target effects and innate immune responses were assessed for each variant.
Conclusions:
- Structural variations in siRNAs can profoundly impact gene silencing efficacy.
- The findings offer critical guidelines for designing effective siRNA variants and complex RNA molecules.
- This systematic analysis advances the understanding of siRNA structure-activity relationships.
Related Concept Videos
01:23RNA Structure
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
01:19RNA Structure
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
01:23RNA Structure
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
02:30siRNA - 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...
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...
01:53RNA Stability
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
01:53RNA Stability
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...