TINA Monomer Stabilizes Hoogsteen Triplexes
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Solution Overview
Problem
Current oligonucleotides face challenges in forming stable triplex structures with double-stranded DNA, particularly due to limitations in recognizing homopurine sequences and the instability of pH-sensitive C·G-C Hoogsteen base triples at physiological conditions, which hampers their effectiveness in gene targeting and therapeutic applications.
Innovation Solution
Development of a flexible basestacking monomer with a specific structure that incorporates intercalators, allowing for co-stacking with nucleobases and providing structural rigidity and flexibility, enhancing the stability of triplex and duplex structures by adjusting its position within the nucleic acid helix.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If traditional oligonucleotides are used for triplex formation, then sequence-specific recognition of homopurine sequences is achieved, but thermal stability of triplex structures is insufficient at physiological conditions
Solution Approach 1:
The patent employs composite oligonucleotide structures combining natural nucleotides with modified intercalating monomers (such as pyrene-containing compounds). These composite structures integrate the sequence-specific recognition capability of natural oligonucleotides with the enhanced thermal stability provided by intercalating aromatic systems, resolving the contradiction between specificity and stability.
Solution Approach 2:
The invention modifies physical-chemical parameters of oligonucleotides by incorporating intercalating groups that alter stacking interactions and helix stability. This changes the thermal parameters of triplex formation, enabling stable structures at physiological temperatures while preserving sequence recognition through Hoogsteen base pairing.
2Stability of the object's composition
If C·G-C Hoogsteen base triples are used for triplex formation, then sequence-specific binding is achieved, but pH sensitivity causes instability at physiological conditions
Solution Approach 1:
The patent introduces local modifications at specific positions within the oligonucleotide sequence, placing intercalating monomers at strategic locations to stabilize the triplex structure without disrupting the overall sequence-specific recognition pattern. This localized approach maintains manufacturing precision while improving pH stability.
3Adaptability or versatility
If intercalating pseudo-nucleotides are incorporated into oligonucleotides, then discrimination between DNA and RNA is improved, but capability of triplex formation is reduced
Solution Approach 1:
The invention segments the oligonucleotide structure into distinct functional domains: regions with intercalating pseudo-nucleotides for DNA/RNA discrimination and regions with standard nucleotides for triplex formation. This segmentation allows each domain to perform its specialized function without compromising the other.
Solution Approach 2:
The patent uses intercalating monomers as intermediary elements that mediate between the requirements for DNA/RNA discrimination and triplex formation capability. These intermediaries provide stacking interactions that stabilize triplexes while maintaining the discriminatory properties of pseudo-nucleotides.
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 flexible basestacking monomer significantly increases the thermal stability of Hoogsteen-type triplexes and duplexes, enabling sequence-specific recognition and modulation of nucleic acids, while maintaining discrimination between different types of nucleic acids, thus enhancing their utility in detection and therapeutic applications.
Implementation Method 1
a flexible basestacking monomer which can be incorporated into an oligonucleotide providing triplex forming oligonucleotides (TFOs) capable of binding sequence specifically with target double stranded or single stranded nucleic acids to form triple helices of very high thermal stability
Data Source
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AI summary
The present invention describes a flexible basestacking monomer that can be incorporated into an oligonucleotide or oligonucleotide analogue, as well as triplex forming oligonucleotides comprising the flexible basestacking monomer. Triplex forming oligonucleotides of the invention are capable of binding sequence specifically to doublestranded target nucleic acids and are therefore of interest for modulation of the activity of target nucleic acids and also detection of target nucleic acids.