Methods and compositions for backscattering interferometry
Inventors
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Assignees
Vanderbilt University • Base Pair Biotechnologies Inc
Member
Base Pair BiotechnologiesBase Pair Biotechnologies specializes in custom aptamer discovery and development for research, diagnostics, therapeutics, and industrial applications. The company leverages proprietary multiplex selection, advanced bioinformatics, and chemical modification techniques to develop high-affinity and selective nucleic acid aptamers. Base Pair enables affinity reagent development, biosensor design, and molecular detection for a broad range of targets and partners across academia and industry.
Base Pair Biotechnologies specializes in custom aptamer discovery and development for research, diagnostics, therapeutics, and industrial applications. The company leverages proprietary multiplex selection, advanced bioinformatics, and chemical modification techniques to develop high-affinity and selective nucleic acid aptamers. Base Pair enables affinity reagent development, biosensor design, and molecular detection for a broad range of targets and partners across academia and industry.
Publication Number
US-9963706-B2
Publication Date
2018-05-08
Expiration Date
Abstract
The present invention relates to methods and compositions for enhancing backscattering interferometry (BSI) in detection of biomolecular interactions, particularly to methods and compositions for enhancing BSI utilizing label-free aptamers, and more particularly to methods and compositions for enhancing BSI utilizing high conformational change aptamers, which may change in conformation when the aptamers bind to their target molecules.
Core Innovation
The present invention relates to methods and compositions for enhancing backscattering interferometry (BSI) in detection of biomolecular interactions, particularly to methods and compositions for enhancing BSI utilizing label-free aptamers, and more particularly to methods and compositions for enhancing BSI utilizing high conformational change aptamers, which may change in conformation when the aptamers bind to their target molecules. In one aspect of the invention, methods and compositions for enhancing BSI may employ label-free aptamers which may generally exhibit a large conformational change between their free, unbound state and their bound state when bound to their target molecule. BSI signals may detect when a molecule undergoes changes in conformation, hydration shell, hydration, etc., and thus may detect a conformational change of an aptamer upon binding a target, as well as any changes in hydration, hydration shell, etc. that may also occur.
Characterization of the interaction between aptamers and their target molecules is described as being of interest because these interactions have broad applications. Two common methods of measuring binding affinity are surface plasmon resonance (SPR) and biolayer interferometry (BLI). SPR is described as a heterogeneous method that requires complicated surface chemistry, immobilization, possible modification of one of the species being examined, and expensive gold-plated slides, and BLI is described as relying on surface immobilization and suffering from similar problems to SPR. The invention addresses enhancing BSI as a label-free, free-solution alternative for detecting conformational and related changes associated with aptamer-target binding.
Claims Coverage
The specification includes one independent method claim. The independent claim discloses four main inventive features related to a hairpin aptamer structure, a contacting step, BSI measurement before and after contacting, and stem dehybridization eliciting a detectable conformational change.
Hairpin aptamer with self-hybridizing stem and non-self-hybridizing loop
Contacting a hairpin aptamer with a sample containing a target molecule, said hairpin having a non-self-hybridizing loop region and self-hybridizing stem region, and comprising a non-naturally occurring sequence.
Contacting hairpin aptamer with sample containing target molecule
Contacting a hairpin aptamer with a sample containing a target molecule.
BSI signal change measurement before and after contacting
Measuring a backscattering interferometry (BSI) signal change before and after contacting said hairpin aptamer with said sample.
Stem dehybridization eliciting conformational change detectable as higher BSI signal
Wherein said self-hybridizing stem region dehybridizes upon binding of said hairpin aptamer to said target molecule and elicits a conformational change in said hairpin aptamer which is detectable as a higher BSI signal after said binding.
The independent claim centers on a hairpin aptamer structure (non-self-hybridizing loop and self-hybridizing stem with a non-naturally occurring sequence), a contacting step with a target-containing sample, measurement of BSI signal change before and after contacting, and a stem dehybridization that elicits a conformational change detectable as a higher BSI signal.
Stated Advantages
Enhancing backscattering interferometry (BSI) in detection of biomolecular interactions using label-free aptamers.
Utilizing high conformational change aptamers to generate detectable BSI signal changes upon target binding.
BSI as a label-free, free-solution technology that allows for a broad range of binding affinities to be measured without a priori knowledge of the binding system.
No need for surface-immobilization or labeling to characterize a binding interaction quantitatively using BSI.
Documented Applications
Detection of biomolecular interactions using backscattering interferometry (BSI).
Use of aptamers as sensors, therapeutic tools, and cellular process regulators, and to guide drugs to their specific cellular targets.
In vivo and diagnostic applications of aptamers.
Measuring binding affinity across a broad range of binding affinities (e.g., pM-mM) using BSI.
Detection of specific targets exemplified by tenofovir and p24 binding to aptamers as documented examples.
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