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Single-molecule mechanical fingerprinting with DNA nanoswitch calipers

  • 1.

    Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).

    CAS 
    Article 

    Google Scholar 

  • 2.

    Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).

    Article 
    CAS 

    Google Scholar 

  • 3.

    Callahan, N., Tullman, J., Kelman, Z. & Marino, J. Strategies for development of a next-generation protein sequencing platform. Trends Biochem. Sci. 45, 76–89 (2020).

    CAS 
    Article 

    Google Scholar 

  • 4.

    Timp, W. & Timp, G. Beyond mass spectrometry, the next step in proteomics. Sci. Adv. 6, eaax8978 (2020).

    CAS 
    Article 

    Google Scholar 

  • 5.

    Alfaro, J. A. et al. The emerging landscape of single-molecule protein sequencing technologies. Nat. Methods 18, 604–617 (2021).

    CAS 
    Article 

    Google Scholar 

  • 6.

    Swaminathan, J., Boulgakov, A. A. & Marcotte, E. M. A theoretical justification for single molecule peptide sequencing. PLoS Comput. Biol. 11, e1004080 (2015).

    Article 
    CAS 

    Google Scholar 

  • 7.

    Yao, Y., Docter, M., van Ginkel, J., de Ridder, D. & Joo, C. Single-molecule protein sequencing through fingerprinting: computational assessment. Phys. Biol. 12, 055003 (2015).

    Article 
    CAS 

    Google Scholar 

  • 8.

    Ohayon, S., Girsault, A., Nasser, M., Shen-Orr, S. & Meller, A. Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput. Biol. 15, e1007067 (2019).

    CAS 
    Article 

    Google Scholar 

  • 9.

    van Ginkel, J. et al. Single-molecule peptide fingerprinting. Proc. Natl Acad. Sci. USA 115, 3338 (2018).

    Article 
    CAS 

    Google Scholar 

  • 10.

    Swaminathan, J. et al. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1082 (2018).

    CAS 
    Article 

    Google Scholar 

  • 11.

    Rosen, C. B., Rodriguez-Larrea, D. & Bayley, H. Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat. Biotechnol. 32, 179–181 (2014).

    CAS 
    Article 

    Google Scholar 

  • 12.

    Kennedy, E., Dong, Z., Tennant, C. & Timp, G. Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore. Nat. Nanotechnol. 11, 968–976 (2016).

    CAS 
    Article 

    Google Scholar 

  • 13.

    Restrepo-Pérez, L., Wong, C. H., Maglia, G., Dekker, C. & Joo, C. Label-free detection of post-translational modifications with a nanopore. Nano Lett. 19, 7957–7964 (2019).

    Article 
    CAS 

    Google Scholar 

  • 14.

    Ouldali, H. et al. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat. Biotechnol. 38, 176–181 (2020).

    CAS 
    Article 

    Google Scholar 

  • 15.

    Zhao, Y. et al. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. Nat. Nanotechnol. 9, 466–473 (2014).

    CAS 
    Article 

    Google Scholar 

  • 16.

    Ohshiro, T. et al. Detection of post-translational modifications in single peptides using electron tunnelling currents. Nat. Nanotechnol. 9, 835–840 (2014).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Koussa, M. A., Halvorsen, K., Ward, A. & Wong, W. P. DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis. Nat. Methods 12, 123–126 (2014).

    Google Scholar 

  • 18.

    Halvorsen, K., Schaak, D. & Wong, W. P. Nanoengineering a single-molecule mechanical switch using DNA self-assembly. Nanotechnology 22, 494005 (2011).

    Article 

    Google Scholar 

  • 19.

    Yang, D., Ward, A., Halvorsen, K. & Wong, W. P. Multiplexed single-molecule force spectroscopy using a centrifuge. Nat. Commun. 7, 11026 (2016).

    CAS 
    Article 

    Google Scholar 

  • 20.

    Kim, J., Zhang, C.-Z., Zhang, X. & Springer, T. A. A mechanically stabilized receptor–ligand flex-bond important in the vasculature. Nature 466, 992–995 (2010).

    CAS 
    Article 

    Google Scholar 

  • 21.

    Pfitzner, E. et al. Rigid DNA beams for high-resolution single-molecule mechanics. Angew. Chem. Int. Ed. 52, 7766–7771 (2013).

    CAS 
    Article 

    Google Scholar 

  • 22.

    Kilchherr, F. et al. Single-molecule dissection of stacking forces in DNA. Science 353, aaf5508 (2016).

  • 23.

    Kostrz, D. et al. A modular DNA scaffold to study protein–protein interactions at single-molecule resolution. Nat. Nanotechnol. 14, 988–993 (2019).

    CAS 
    Article 

    Google Scholar 

  • 24.

    Gosse, C., Strick, T. R. & Kostrz, D. Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations. Curr. Opin. Chem. Biol. 53, 192–203 (2019).

    CAS 
    Article 

    Google Scholar 

  • 25.

    Ma, X. et al. Interactions between PHD3-bromo of MLL1 and H3K4me3 revealed by single-molecule magnetic tweezers in a parallel DNA circuit. Bioconjug Chem. 30, 2998–3006 (2019).

    CAS 
    Article 

    Google Scholar 

  • 26.

    Hatch, K., Danilowicz, C., Coljee, V. & Prentiss, M. Demonstration that the shear force required to separate short double-stranded DNA does not increase significantly with sequence length for sequences longer than 25 base pairs. Phys. Rev. E. 78, 011920 (2008).

    CAS 
    Article 

    Google Scholar 

  • 27.

    Watson, J. D. & Crick, F. H. C. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953).

    CAS 
    Article 

    Google Scholar 

  • 28.

    Woodside, M. T. et al. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc. Natl Acad. Sci. USA 103, 6190–6195 (2006).

    CAS 
    Article 

    Google Scholar 

  • 29.

    Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. Entropic elasticity of λ-phage DNA. Science 265, 1599–1600 (1994).

    CAS 
    Article 

    Google Scholar 

  • 30.

    Abello, N., Kerstjens, H. A. M., Postma, D. S. & Bischoff, R. Selective acylation of primary amines in peptides and proteins. J. Proteome Res. 6, 4770–4776 (2007).

    CAS 
    Article 

    Google Scholar 

  • 31.

    Zhang, X., Halvorsen, K., Zhang, C.-Z., Wong, W. P. & Springer, T. A. Mechanoenzymatic cleavage of the ultralarge vascular protein von Willebrand factor. Science 324, 1330–1334 (2009).

    CAS 
    Article 

    Google Scholar 

  • 32.

    Oesterhelt, F. et al. Unfolding pathways of individual bacteriorhodopsins. Science 288, 143–146 (2000).

    CAS 
    Article 

    Google Scholar 

  • 33.

    Carrion-Vazquez, M. et al. The mechanical stability of ubiquitin is linkage dependent. Nat. Struct. Mol. Biol. 10, 738–743 (2003).

    CAS 
    Article 

    Google Scholar 

  • 34.

    Oda, E. et al. Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis. Science 288, 1053 (2000).

    CAS 
    Article 

    Google Scholar 

  • 35.

    Czabotar, P. E. et al. Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proc. Natl Acad. Sci. USA 104, 6217 (2007).

    CAS 
    Article 

    Google Scholar 

  • 36.

    Sattler, M. et al. Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science 275, 983–986 (1997).

    CAS 
    Article 

    Google Scholar 

  • 37.

    Apweiler, R. et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004).

    CAS 
    Article 

    Google Scholar 

  • 38.

    Adamczyk, M., Gebler, J. C. & Wu, J. Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1481–1488 (2001).

    CAS 
    Article 

    Google Scholar 

  • 39.

    Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004).

    CAS 
    Article 

    Google Scholar 

  • 40.

    Phatnani, H. P. & Greenleaf, A. L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006).

    CAS 
    Article 

    Google Scholar 

  • 41.

    Kim, M., Suh, H., Cho, E. J. & Buratowski, S. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J. Biol. Chem. 284, 26421–26426 (2009).

    CAS 
    Article 

    Google Scholar 

  • 42.

    Eick, D. & Geyer, M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem. Rev. 113, 8456–8490 (2013).

    CAS 
    Article 

    Google Scholar 

  • 43.

    Knight, Z. A. et al. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol. 21, 1047–1054 (2003).

    CAS 
    Article 

    Google Scholar 

  • 44.

    Ribeck, N. & Saleh, O. A. Multiplexed single-molecule measurements with magnetic tweezers. Rev. Sci. Instrum. 79, 094301 (2008).

    Article 
    CAS 

    Google Scholar 

  • 45.

    De Vlaminck, I. et al. Highly parallel magnetic tweezers by targeted DNA tethering. Nano Lett. 11, 5489–5493 (2011).

    Article 
    CAS 

    Google Scholar 

  • 46.

    Cnossen, J. P., Dulin, D. & Dekker, N. H. An optimized software framework for real-time, high-throughput tracking of spherical beads. Rev. Sci. Instrum. 85, 103712 (2014).

    CAS 
    Article 

    Google Scholar 

  • 47.

    Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122 (1992).

    CAS 
    Article 

    Google Scholar 

  • 48.

    Danilowicz, C., Greenfield, D. & Prentiss, M. Dissociation of ligand–receptor complexes using magnetic tweezers. Anal. Chem. 77, 3023–3028 (2005).

    CAS 
    Article 

    Google Scholar 

  • 49.

    Shon, M. J., Rah, S.-H. & Yoon, T.-Y. Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers. Sci. Adv. 5, eaav1697 (2019).

    Article 
    CAS 

    Google Scholar 

  • 50.

    Sen, Y.-H., Jain, T., Aguilar, C. A. & Karnik, R. Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements. Lab. Chip 12, 1094–1101 (2012).

    CAS 
    Article 

    Google Scholar 

  • 51.

    Keyser, U. F. et al. Direct force measurements on DNA in a solid-state nanopore. Nat. Phys. 2, 473–477 (2006).

    CAS 
    Article 

    Google Scholar 

  • 52.

    Mulhall, E. M. et al. Single-molecule force spectroscopy reveals the dynamic strength of the hair-cell tip-link connection. Nat. Commun. 12, 849 (2021).

    CAS 
    Article 

    Google Scholar 

  • 53.

    Bustamante, C., Chemla, Y. R. & Moffitt, J. R. High-resolution dual-trap optical tweezers with differential detection: instrument design. Cold Spring Harb. 2009, pdb.ip73 (2009).

    Google Scholar 

  • 54.

    Lipfert, J., Hao, X. & Dekker, N. H. Quantitative modeling and optimization of magnetic tweezers. Biophys. J. 96, 5040–5049 (2009).

    CAS 
    Article 

    Google Scholar 

  • 55.

    Dulin, D. et al. High spatiotemporal-resolution magnetic tweezers: calibration and applications for DNA dynamics. Biophys. J. 109, 2113–2125 (2015).

    CAS 
    Article 

    Google Scholar 

  • 56.

    De Vlaminck, I., Henighan, T., van Loenhout, M. T. J., Burnham, D. R. & Dekker, C. Magnetic forces and DNA mechanics in multiplexed magnetic tweezers. PLoS ONE 7, e41432 (2012).

    Article 
    CAS 

    Google Scholar 

  • 57.

    Yu, Z. et al. A force calibration standard for magnetic tweezers. Rev. Sci. Instrum. 85, 123114 (2014).

    Article 
    CAS 

    Google Scholar 

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