Stem-Loop Artificial sRNA for Bacterial Gene Silencing
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Solution Overview
Problem
Current methods for silencing specific genes in bacteria are inefficient, lacking effective strategies for gene knockdown or silencing, unlike in eukaryotic cells where short interfering RNAs (siRNAs) are used.
Innovation Solution
A nucleic acid complex with a stem-loop structure is designed, comprising a first nucleic acid molecule, a second nucleic acid molecule, and a target recognition sequence linked between them, which is delivered to prokaryotes to effectively silence bacterial genes by conferring single-strandedness and stability to target recognition sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If artificial sRNA is used for gene silencing in bacteria, then gene silencing capability is improved, but delivery efficiency and stability of target recognition sequences are insufficient
Solution Approach 1:
The target recognition sequence is nested within the stem-loop structure of the nucleic acid molecule. The stem-loop structure acts as a scaffold that houses the target recognition sequence, protecting it from degradation while maintaining its functional capability to bind target mRNA. This nesting approach resolves the contradiction by providing stability through the structural scaffold without compromising the silencing function.
Solution Approach 2:
The invention changes the structural parameters of the nucleic acid molecule by introducing a stem-loop configuration with specific base-pairing regions. This structural modification enhances the stability and persistence of the target recognition sequence in the bacterial cell, thereby improving delivery efficiency and silencing reliability simultaneously.
2Reliability
If target recognition sequences are delivered to prokaryotes, then gene silencing effect is improved, but sequence stability and persistence are insufficient
Solution Approach 1:
The target recognition sequence is embedded within the stem-loop structure, which acts as a protective scaffold. This nested configuration prevents rapid degradation of the sequence, extending its persistence in the bacterial cell and thereby improving the duration of gene silencing action.
Solution Approach 2:
The stem-loop structure provides continuous stability to the target recognition sequence, ensuring prolonged presence and activity within the bacterial cell. This continuous structural support maintains the sequence's functional capability over extended periods, achieving sustained gene silencing effects.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The nucleic acid complex efficiently inhibits gene expression by forming complementary bindings to ribosome binding sites, reducing mRNA levels of target genes, such as cspE and ompF, demonstrating a significant silencing effect.
Implementation Method 1
The nucleic acid complex efficiently inhibits gene expression by forming complementary bindings to ribosome binding sites
Data Source
AI summary
A nucleic acid molecule comprising a stem-loop structure, a nucleic acid complex comprising the nucleic acid molecule, a composition for delivering a target recognition sequence, and the composition comprising the nucleic acid complex. An artificial small ribonucleic acid of the stem-loop structure stably maintains single-strandedness of a target recognition sequence which interacts with a nucleic acid of interest for a gene of interest of a prokaryote, thereby providing a nucleic acid complex for effective silencing of the gene of interest.