Related Experiment Video
Updated: Jul 13, 2026

07:02
An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
Effect of target secondary structure on RNAi efficiency.
Yu Shao1, Chi Yu Chan, Anil Maliyekkel
1Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA.
Summary
Small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) efficiency in gene knockdown is improved by considering target accessibility and duplex asymmetry. These factors significantly enhance RNA interference (RNAi) efficacy for better gene silencing outcomes.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- RNA interference (RNAi) is a key gene silencing mechanism.
- Small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) are widely used for gene knockdown.
- RNAi efficiency varies significantly, necessitating optimization strategies.
Purpose of the Study:
- To investigate factors influencing RNAi efficiency, focusing on target accessibility and siRNA duplex asymmetry.
- To identify design criteria for improving siRNA and shRNA efficacy in gene knockdown studies.
Main Methods:
- Analysis of target disruption energy, a measure of target accessibility, based on predicted secondary structures using the Sfold program.
- Evaluation of siRNA duplex asymmetry in relation to RNA-induced silencing complex (RISC) assembly.
- Statistical analysis of 100 siRNAs and 101 shRNAs targeting 103 human genes.
Main Results:
- Target disruption energy is a significant determinant of RNAi activity.
- siRNA duplex asymmetry is crucial for efficient RISC assembly.
- Target accessibility and duplex asymmetry can improve knockdown levels by approximately 40% and 26%, respectively.
Conclusions:
- Duplex asymmetry impacts RISC assembly upstream, while target accessibility affects downstream target recognition.
- Optimizing target accessibility and duplex asymmetry can significantly enhance gene knockdown via RNAi.
- The findings provide criteria for designing more effective siRNAs and shRNAs.
Related Concept Videos
RNA 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...
RNA 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...
RNA 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...
Nucleic Acid Structure
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
DNA Structure
DNA has a double-helix structure. The...
RNA 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...
RNA 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...

