INTmer Chimeric Oligonucleotide for Undruggable Gene Silencing
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Solution Overview
Problem
Current technologies lack effective methods for modulating the expression of nearly 17,000 protein-coding genes that are deemed 'undruggable' by small molecules.
Innovation Solution
The use of Initiation of Transcription GAPmers (INTmers), which are nucleic acid molecules comprising 14-22 nucleotides with a central DNA core flanked by RNA on each side, to specifically silence gene expression by hybridizing to nascent mRNA transcripts and inducing cleavage by RNase H1.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If small molecules are used to modulate gene expression, then druggable genes can be targeted, but nearly 17,000 protein-coding genes remain undruggable
Solution Approach 1:
The patent uses INTmers as intermediary molecules that bridge the gap between available therapeutic agents and previously undruggable genes. These chimeric oligonucleotides with DNA/RNA hybrid structure serve as mediators that can specifically bind to nascent mRNA transcripts through RNA-DNA hybridization, enabling modulation of gene expression for targets that small molecules cannot address.
Solution Approach 2:
The invention changes the chemical parameters of the oligonucleotide structure by creating a chimeric DNA/RNA hybrid molecule with specific modifications. The INTmer comprises a central DNA core flanked by RNA segments, with modified nucleotides including phosphorothioate linkages and 2'-O-methoxy RNA, altering physical and chemical properties to achieve both stability and specific binding to nascent transcripts.
2Reliability
If INTmers hybridize to nascent mRNA transcripts at the 5' end, then gene expression is effectively silenced, but precise localization within the first 350 base pairs is required
Solution Approach 1:
The INTmer design applies local quality by concentrating the complementary DNA sequence specifically at positions that hybridize to the nascent mRNA transcript within the first 350 base pairs from the 5' end. This localized complementarity ensures specific binding to the transcription initiation region while the flanking RNA portions provide stability and directional orientation.
Solution Approach 2:
The INTmer is designed to bind to the nascent mRNA transcript during or immediately after transcription initiation, before the transcript is fully processed. By targeting the 5' end region within the first 350 base pairs, the INTmer acts preliminarily to prevent proper gene expression from occurring, silencing the gene at its source.
3Object-generated harmful factors
If the INTmer comprises a central DNA core flanked by RNA, then specific cleavage by RNase H1 is enabled, but the nucleic acid structure becomes more complex
Solution Approach 1:
The INTmer structure is segmented into distinct functional regions: a central DNA core segment that is complementary to the target nascent mRNA and serves as the substrate for RNase H1 cleavage, flanked by RNA segments that provide stability and directional orientation. This segmentation allows each portion to perform its specific function while working together as a unified therapeutic agent.
Solution Approach 2:
The INTmer is a composite nucleic acid molecule combining DNA and RNA components in a chimeric structure. The central DNA core is flanked by RNA segments, creating a hybrid molecule that leverages the properties of both nucleic acid types - the stability and RNase H1 recognition of DNA, and the structural flexibility and cellular compatibility of RNA.
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
INTmers effectively silence gene expression by cleaving nascent RNA transcripts at the transcription initiation site, providing a novel approach to modulating 'undruggable' genes and treating diseases associated with aberrant gene expression.
Implementation Method 1
allowing the INTmer to hybridize to the nascent mRNA transcript of the gene of interest, wherein said INTmer hybridizes within the first 350 base pairs (for examples, the first 150 base pairs) of a 5′ end of the nascent mRNA transcript
Implementation Method 2
cleaving the nascent RNA:INTmer duplex, thereby silencing expression of the gene of interest
Data Source
AI summary
The present disclosure relates to methods of silencing expression of genes and uses thereof for treating diseases. Specifically, disclosed herein are Initiation of Transcription GAPmer (INTmers), wherein said INTmers comprise a nucleic acid molecule comprising 14-22 nucleotides, and further wherein said nucleic acid molecule comprises a central core of DNA flanked by RNA on each side.