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US 2023/0146476 A1Published application
Nanoswitch caliper trains for high-throughput, high-resolution structural analysis of biomolecules
AssigneesPresident and Fellows of Harvard College, Children's Medical Center Corporation, Dana-Farber Cancer Institute, Inc.
InventorsJames I. MacDonald, Michael H. Raez, William M. Shih, Wesley Philip Wong
Life of this patent
Estimating the term…
Abstract
Provided herein are compositions and methods for determining the structure of individual targets by determining long-range distances within such targets.
Claims30
A composition comprising
- a nucleic acid having a plurality of single-stranded branched oligonucleotides, covalently attached using non-phosphodiester bond, at pre-determined distances along its length.
A composition comprising
- a nucleic acid-protein complex comprising a nucleic acid having a plurality of single-stranded branched oligonucleotides, covalently attached using non-phosphodiester bond, at pre-determined distances along its length, a first subset of branched oligonucleotides having reporter moieties at their free ends, and a protein attached to first and second adjacent, internal branched oligonucleotides.
A method of performing distance measurements of a protein, comprising
- providing a nucleic acid-protein complex comprising a nucleic acid having a plurality of single-stranded branched oligonucleotides (T1-T6), covalently attached using non-phosphodiester bonds, at pre-determined distances along its length, a first subset of branched oligonucleotides having reporter moieties at their free ends (T1, T2, T5, T6), and a protein having first and second single-stranded nucleic acid handles (SS nucleic acid handles) attached to first and second adjacent, internal branched oligonucleotides (T3, T4), wherein a first end of the nucleic acid is attached to a solid support and a second end of the nucleic acid is attached to a bead,
- applying a force on the complex in the direction of the bead, and
- (i) detecting location of the first subset of branched oligonucleotides under force, optionally relative to location of the first subset of branched oligonucleotides in the absence of force, and/or
- (ii) measuring distance between adjacent reporter moieties under force, optionally relative to distance between adjacent reporter moieties in the absence of force,
- wherein a change in location or a change in distance represents a distance between the first and second SS nucleic acid handles.
2 more elements
A method of performing distance measurements of a protein, comprising
- providing a nucleic acid-protein complex comprising (1) a nucleic acid covalently attached using non-phosphodiester bonds, at pre-determined distances along its length, to six single-stranded branched oligonucleotides (T1-T6), the first, second, fifth and sixth branched oligonucleotides (T1, T2, T5, T6) having reporter moieties at their free ends, and (2) a protein having first and second single-stranded nucleic acid handles (SS nucleic acid handles) attached to the third and fourth branched oligonucleotides (T3, T4), wherein a first end of the nucleic acid is attached to a solid support and a second end of the nucleic acid is attached to a bead,
- applying a force on the complex in the direction of the bead, and
- (i) detecting the location of the reporter moieties attached to T1, T2, T5 and T6 under force, optionally relative to their location in the absence of force, and/or
- (ii) measuring distance between reporter moieties attached to T1, T2, T5 and T6 under force, optionally relative to said distance in the absence of force,
- wherein a change in location or a change in distance under force represents a distance between the first and second SS nucleic acid handles on the protein.
2 more elements
Dependencies are inferred from the claim text.