1. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers
- Author
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Andrew Ward, Darren Yang, Wesley P. Wong, Serkan Cabi, Elisha Krieg, Bhavik Nathwani, Prakash Shrestha, Yi Luo, Toma E. Tomov, William M. Shih, James I. MacDonald, Hans T. Bergal, and Alexander Johnson-Buck
- Subjects
chemistry.chemical_classification ,Magnetic tweezers ,Materials science ,Biomolecule ,Biomedical Engineering ,Force spectroscopy ,Bioengineering ,Nanotechnology ,Condensed Matter Physics ,Proteomics ,Atomic and Molecular Physics, and Optics ,chemistry.chemical_compound ,Optical tweezers ,chemistry ,DNA nanotechnology ,Nanobiotechnology ,General Materials Science ,Electrical and Electronic Engineering ,DNA - Abstract
Decoding the identity of biomolecules from trace samples is a longstanding goal in the field of biotechnology. Advances in DNA analysis have substantially affected clinical practice and basic research, but corresponding developments for proteins face challenges due to their relative complexity and our inability to amplify them. Despite progress in methods such as mass spectrometry and mass cytometry, single-molecule protein identification remains a highly challenging objective. Towards this end, we combine DNA nanotechnology with single-molecule force spectroscopy to create a mechanically reconfigurable DNA nanoswitch caliper capable of measuring multiple coordinates on single biomolecules with atomic resolution. Using optical tweezers, we demonstrate absolute distance measurements with angstrom-level precision for both DNA and peptides, and using multiplexed magnetic tweezers, we demonstrate quantification of relative abundance in mixed samples. Measuring distances between DNA-labelled residues, we perform single-molecule fingerprinting of synthetic and natural peptides, and show discrimination, within a heterogeneous population, between different posttranslational modifications. DNA nanoswitch calipers are a powerful and accessible tool for characterizing distances within nanoscale complexes that will enable new applications in fields such as single-molecule proteomics. DNA nanoswitch calipers can measure distances within single molecules with atomic resolution. Applied to single-molecule proteomics, they can enable the identification and quantification of molecules in trace samples via mechanical fingerprinting.
- Published
- 2021