2'-5' Linked IsoDNA G-Quadruplex Aptamers
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Solution Overview
Problem
Current technologies lack stable, non-genetic guanine-rich 2′-5′ linked isoDNA oligomers capable of forming unimolecular antiparallel G-quadruplex structures, which are essential for maintaining biological molecular recognition and functional ability in therapeutics and diagnostics.
Innovation Solution
Development of stable, non-genetic guanine-rich 2′-5′ linked isoDNA sequences and their process of preparation, including synthesizing 3′-5′-oligonucleotides with β-cyanoethyl phosphoramidite chemistry and replacing 3′-5′-phosphodiester linkages with 2′-5′-phosphodiester linkages, followed by modifications such as uridine substitution in the TGT loop to enhance stability and form unimolecular antiparallel G-quadruplexes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If 3′-5′-phosphodiester linkages are used in DNA sequences, then stable duplexes and functional molecular recognition are achieved, but the sequences cannot form unimolecular antiparallel G-quadruplex structures
Solution Approach 1:
The patent changes the phosphodiester linkage parameter from the conventional 3′-5′ configuration to a non-genetic 2′-5′ configuration. This parameter change enables the DNA sequence to form unimolecular antiparallel G-quadruplex structures while maintaining duplex stability through the anomeric effect and extended backbone geometry provided by the 2′-5′ linkage.
2Adaptability or versatility
If 2′-5′ linked isoDNA sequences are synthesized, then unimolecular antiparallel G-quadruplex structures are formed, but thermal stability is lower compared to conventional DNA:DNA duplexes
Solution Approach 1:
The patent creates a hybrid structure combining 2′-5′ linked isoDNA with conventional 3′-5′ linked DNA or RNA sequences. This composite approach allows the isoDNA portion to form G-quadruplex structures while the conventional portion provides thermal stability through standard base pairing, achieving both structural versatility and thermal stability.
3Stability of the object's composition
If backbone modifications are introduced to enhance stability, then structural topology is maintained, but synthesis complexity increases
Solution Approach 1:
The patent divides the oligonucleotide sequence into distinct segments with different backbone linkages - 2′-5′ linked isoDNA segments for G-quadruplex formation and 3′-5′ linked conventional DNA/RNA segments for stability. This segmentation allows each segment to be synthesized using optimized methods and then joined together, reducing overall synthesis complexity compared to modifying a single homogeneous backbone.
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 resulting 2′-5′ linked isoDNA oligomers maintain biological molecular recognition, exhibit improved stability, and are useful in therapeutics and diagnostics, particularly in treating deep vein thrombosis by forming stable G-quadruplex structures that retain functional ability.
Implementation Method 1
Four guanine bases associate through Hoogsteen hydrogen bonding to form a square planar structure called a guanine tetrad, and two or more guanine tetrads can stack on top of each other to form a G-quadruplex
Implementation Method 2
The 2′-5′ linkages maintain an extended backbone geometry due to the anomeric effect and the O4′-C1′-C2′-O2′ gauche effect on the substituted sugar leading to the N-type geometry sugar conformations
Implementation Method 3
The G-quadruplex structures as telomeres at the chromosomal ends are meant for conservation of genetic information during repeating cell cycles and are also capable of specific interactions with proteins
Data Source
AI summary
The present invention relates to G-quadruplex forming isoDNA aptamers and a process for the preparation thereof. The present invention further relates to a stable, non-genetic, guanine rich 2′-5′ linked isoDNA selected from 3′ deoxy 2′-5′ isoDNA and 3′ deoxy 2′-5′ isoDNA-isoRNA hybrid. The instant 2′-5′ linked isoDNA such as the thrombin binding aptamer (isoTBA) can be used in deep vein thrombosis, where prolonged anticoagulant activity is required.