Covalently Tethered Double-Stranded DNA for Low-Force Interaction Measurement
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing molecular interaction studies face challenges with non-specific interactions, conformational constraints, limited flexibility and rigidity, and variability in molecular properties, making it difficult to measure interactions at low forces and diverse molecular structures effectively.
Innovation Solution
A double-stranded DNA molecule connected by covalent bonds other than phosphodiester, phosphorothioate, or phosphoramidate bonds, allowing for flexible and stable molecular interactions with adjustable lengths and supports, enabling characterization of interactions at low forces and diverse molecular compositions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Object-affected harmful factors
If a polypeptide tether is used to connect test molecules to supports, then the test molecules can be indirectly attached to reduce non-specific interactions, but the tether length is limited to about 100 amino acids which increases the effective concentration of test molecules and limits the study of fast associations
Solution Approach 1:
The patent changes the chemical composition parameter from polypeptide to nucleotide-based tethers (DNA or RNA), which have different physical and chemical properties. This allows the tether to be longer (reducing effective concentration) while maintaining stability and reducing non-specific interactions, thereby expanding the measurable association rate constant range.
Solution Approach 2:
The patent uses composite molecular structures combining nucleotide tethers with test molecules and supports. This composite approach leverages the stability and low non-specific interaction properties of nucleic acids while enabling flexible length adjustment to optimize for different interaction kinetics.
2Ease of manufacture
If globular proteins are used to attach test molecules to supports, then test molecules can be directly attached, but this causes artifacts from support-support or molecule-support non-specific interactions
Solution Approach 1:
The patent introduces nucleotide-based tethers as intermediary molecules between the test molecules and the supports. These tethers serve as a mediator that reduces direct contact between test molecules and supports, thereby minimizing non-specific interactions while maintaining the attachment function.
3Adaptability or versatility
If fusion proteins are used to integrate test molecules, then test molecules can be attached to supports, but the type of test molecules that can be integrated is limited and major preparation effort is required
Solution Approach 1:
The patent segments the molecular assembly into separate components: the nucleotide tether and the test molecule. This segmentation allows independent optimization and preparation of each component, reducing the complexity of preparing fusion proteins and enabling greater diversity in test molecule types.
4Quantity of substance
If a short polypeptide tether is used, then the effective concentration of test molecules increases, but this limits the study of molecular associations with fast rate constants
Solution Approach 1:
The patent changes the tether material from polypeptide to nucleotide-based structures, which have different persistence lengths and mechanical properties. This parameter change allows for longer tether lengths that reduce the effective concentration of test molecules, thereby enabling the study of faster associating molecules with higher rate constants.
Data Source
AI summary
The present application relates to a double-stranded DNA molecule comprising a first double-stranded DNA molecule (1) connected to a second double-stranded DNA molecule (2) by at least one covalent bond which is not a phosphodiester, phosphorothioate, phosphoramidate or phosphorodiamidate bond, preferably by a tether, said tether preferably being a double-stranded DNA molecule.