ANRIL-TDO DNA Polynucleotide Triplex Blocking
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Solution Overview
Problem
Current strategies for modulating gene expression, particularly targeting long non-coding RNAs like ANRIL, lack specificity and can cause undesirable effects due to non-specific action, and the mechanisms of ANRIL's genomic recognition and regulation are not fully understood, leading to challenges in addressing pathological conditions such as cancers and cardiovascular diseases.
Innovation Solution
A double-stranded DNA polynucleotide, ANRIL-TDO, is designed to specifically block the formation of triplexes between genomic DNA and ANRIL, allowing for precise modulation of ANRIL's gene regulatory activity by targeting its triplex-mediated recognition, without affecting its stability or expression, and is engineered for enhanced biostability and cellular uptake.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If current strategies for modulating gene expression are used to target ANRIL, then gene expression can be modulated, but specificity is lost and undesirable off-target effects occur
Solution Approach 1:
The patent introduces a double-stranded DNA polynucleotide as an intermediary molecule that specifically binds to ANRIL through triplex formation. This intermediary acts as a bridge between the therapeutic goal (modulating ANRIL activity) and the target (ANRIL), enabling selective modulation without directly interfering with ANRIL's natural functions. The DNA polynucleotide mediates the interaction by forming triplex structures with ANRIL, thereby providing the needed specificity while avoiding off-target effects.
Solution Approach 2:
The patent changes the chemical parameters of the therapeutic agent by using a double-stranded DNA polynucleotide with specific sequence composition and structural properties. The DNA polynucleotide is designed with specific base sequences that complement ANRIL's triplex-forming regions, and its double-stranded structure provides enhanced stability and specificity. By adjusting parameters such as GC content, sequence length, and structural conformation, the patent achieves high-specificity binding to ANRIL while minimizing non-specific interactions.
2Reliability
If ANRIL's gene regulatory activity is blocked to treat pathological conditions, then pathological gene expression is corrected, but normal ANRIL function in non-pathological situations may be affected
Solution Approach 1:
The patent applies partial action by designing the DNA polynucleotide to bind only to specific triplex-forming regions of ANRIL that are involved in pathological gene regulation. Rather than completely blocking all ANRIL functions, the therapy selectively inhibits only the pathological interactions while leaving other physiological functions intact. The DNA polynucleotide is designed with specific sequence targeting the anomalous triplex structures formed in pathological conditions, thereby achieving selective modulation without affecting normal ANRIL activity in non-pathological situations.
3Measurement precision
If triplex formation between DNA and ANRIL is targeted for therapy, then specific gene regulation can be achieved, but the complexity of understanding and designing such specific interactions increases
Solution Approach 1:
The patent applies segmentation by dividing the ANRIL molecule into distinct functional regions, specifically identifying and targeting the triplex-forming regions (TFRs) separately from other functional domains. The DNA polynucleotide is designed to specifically recognize and bind to these segmented TFR regions through complementary base sequencing. This segmentation approach simplifies the design process by focusing on specific targetable regions rather than attempting to modulate the entire ANRIL molecule, thereby reducing design complexity while maintaining high precision in gene targeting.
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
ANRIL-TDO effectively modulates ANRIL's activity in pathological conditions by preventing it from binding to certain genomic loci, thereby selectively impacting genes regulated by ANRIL, reducing the risk of off-target effects and maintaining normal ANRIL function in non-pathological situations, with improved pharmacokinetic properties and immune system avoidance.
Implementation Method 1
These triplexes are non-canonical structures in which a single-stranded RNA (Triplex Forming Oligonucleotide, TFO) accommodates the major groove of the DNA double helix (Triplex Targeting Site, TTS). TTSs correspond exclusively to purine-rich sequences (Adenine-A/Guanine-G) and form non-canonical Hoogsteen or reverse Hoogsteen base pairs with TFO
Implementation Method 2
form non-canonical Hoogsteen or reverse Hoogsteen base pairs with TFO
Data Source
AI summary
The present invention relates to an isolated double stranded DNA polynucleotide that forms triplex with sequence 5′-GGUGGCAGCAAGAGAAAAAUGAGGAAGAAGCAAAAGCGGAAA-3′ (SEQ ID NO: 1) of the long non-coding RNA ANRIL (Antisense Non-coding RNA in the INK4 Locus). It also relates to a vector comprising the double stranded DNA polynucleotide, and to a pharmaceutical composition comprising the double stranded DNA polynucleotide or the vector. The present invention relates as well to the isolated double stranded DNA polynucleotide for use in the treatment of myocardial infarction, aneurysms, stenosis, myocardial infarction, aneurysms, cancers, eye diseases or type 2 diabetes.