Chinese Optics, Volume. 15, Issue 5, 878(2022)

Research progress of single molecule biological detection methods and applications

Wen-chao ZHOU1, Zheng-hao LI1,2, and Jie WU1,2
Author Affiliations
  • 1State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
  • 2University of Chinese Academy of Sciences, Beijing 100049, China
  • show less
    References(93)

    [1] HALL C E. Method for the observation of macromolecules with the electron microscope illustrated with micrographs of DNA[J]. The Journal of Biophysical and Biochemical Cytology, 2, 625-628(1956).

    [2] ROTMAN B. Measurement of activity of single molecules of β -D-galactosidase[J]. Proceedings of the National Academy of Sciences of the United States of America, 47, 1981-1991(1961).

    [3] MILLER H, ZHOU ZH K, SHEPHERD J, et al. Single-molecule techniques in biophysics: a review of the progress in methods and applications[J]. Reports on Progress in Physics, 81, 024601(2018).

    [4] HIRSCHFELD T. Optical microscopic observation of single small molecules[J]. Applied Optics, 15, 2965-2966(1976).

    [5] GELLES J, SCHNAPP B J, SHEETZ M P. Tracking kinesin-driven movements with nanometre-scale precision[J]. Nature, 331, 450-453(1988).

    [6] ORRIT M, BERNARD J. Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal[J]. Physical Review Letters, 65, 2716-2719(1990).

    [7] KNEIPP K, WANG Y, KNEIPP H, et al. Single molecule detection using surface-enhanced Raman scattering (SERS)[J]. Physical Review Letters, 78, 1667-1670(1997).

    [8] LU H P, XUN L, XIE X S. Single molecule enzymatic dynamics[J]. Science, 282, 1877-1882(1998).

    [9] VOGELSTEIN B, KINZLER K W. Digital PCR[J]. Proceedings of the National Academy of Sciences of the United States of America, 96, 9236-9241(1999).

    [10] KOREN S, SCHATZ M C, WALENZ B P, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads[J]. Nature Biotechnology, 30, 693-700(2012).

    [11] GOOTENBERG J S, ABUDAYYEH O O, LEE J W, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2[J]. Science, 356, 438-442(2017).

    [12] FUXREITER M, VENDRUSCOLO M. Generic nature of the condensed states of proteins[J]. Nature Cell Biology, 23, 587-594(2021).

    [13] WANG Y Q, GUAN X Y, ZHANG S Y, et al. Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A[J]. Nature Communications, 12, 3368(2021).

    [14] RUAN J B, XIA SH Y, LIU X, et al. Cryo-EM structure of the gasdermin A3 membrane pore[J]. Nature, 557, 62-67(2018).

    [15] WANG J Z, HU M J, WANG J, et al. Reconstitution and structure of a plant NLR resistosome conferring immunity[J]. Science, 364, eaav5870(2019).

    [16] LANGECKER M, ARNAUT V, MARTIN T G, et al. Synthetic lipid membrane channels formed by designed DNA nanostructures[J]. Science, 338, 932-936(2012).

    [17] KASIANOWICZ J J, BRANDIN E, BRANTON D. Characterization of individual polynucleotide molecules using a membrane channel[J]. Proceedings of the National Academy of Sciences of the United States of America, 93, 13770-13773(1996).

    [18] CHAVIS A E, BRADY K T, HATMAKER G A, et al. Single molecule nanopore spectrometry for peptide detection[J]. ACS Sensors, 2, 1319-1328(2017).

    [19] RAHMAN M M, SAMPAD M J N, HAWKINS A, et al. Recent advances in integrated solid-state nanopore sensors[J]. Lab on a Chip, 21, 3030-3052(2021).

    [20] MACCAFERRIN, BARBILLON G, KOYAAN, et al. Recent advances in plasmonic nanocavities for single-molecule spectroscopy[J]. Nanoscale Advance, 3, 633-642(2021).

    [21] ASSAD O N, GILBOA T, SPITZBERG J, et al. Light-enhancing plasmonic-nanopore biosensor for superior single-molecule detection[J]. Advanced Materials, 29, 1605442(2017).

    [22] BUCHFINK B, REUTER K, DROST H G. Sensitive protein alignments at tree-of-life scale using DIAMOND[J]. Nature Methods, 18, 366-368(2021).

    [23] BELLENGUEZ C, KÜÇÜKALI F, JANSEN I E, et al. New insights into the genetic etiology of Alzheimer's disease and related dementias[J]. Nature Genetics, 54, 412-436(2022).

    [24] DEVESON I W, GONG B SH, LAI K, et al. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology[J]. Nature Biotechnology, 39, 1115-1128(2021).

    [25] [25] BRINKERHOFF H, KANG A S W, LIU J Q, et al.. Infinite rereading of single proteins at singleaminoacid resolution using nanope sequencing[J]. Bixiv, 2021, doi: 10.1126science.abl4381.

    [26] SEN P, GUPTA M. Single nucleotide detection using bilayer MoS2 nanopores with high efficiency[J]. RSC Advances, 11, 6114-6123(2021).

    [27] YAMAZAKI H, HU R, ZHAO Q, et al. Photothermally assisted thinning of silicon nitride membranes for ultrathin asymmetric nanopores[J]. ACS Nano, 12, 12472-12481(2018).

    [28] BURCK N, GILBOA T, GADI A, et al. Nanopore identification of single nucleotide mutations in circulating tumor DNA by multiplexed ligation[J]. Clinical Chemistry, 67, 753-762(2021).

    [29] YUAN B, LI SH, YING Y L, et al. The analysis of single cysteine molecules with an aerolysin nanopore[J]. Analyst, 145, 1179-1183(2020).

    [30] PIGUET F, OULDALI H, PASTORIZA-GALLEGO M, et al. Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore[J]. Nature Communications, 9, 966(2018).

    [31] CAO C, CIRAUQUI N, MARCAIDA M J, et al. Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores[J]. Nature communications, 10, 1-11(2019).

    [32] ZHANG SH L, HUANG G, VERSLOOT R C A, et al. Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins[J]. Nature Chemistry, 13, 1192-1199(2021).

    [33] LI M Y, YING Y L, YU J, et al. Revisiting the origin of nanopore current blockage for volume difference sensing at the atomic level[J]. JACS Au, 1, 967-976(2021).

    [34] LEIRS K, KUMAR P T, DECROP D, et al. Bioassay development for ultrasensitive detection of influenza a nucleoprotein using digital ELISA[J]. Analytical Chemistry, 88, 8450-8458(2016).

    [35] SHAFAGH R Z, DECROP D, VEN K, et al. Reaction injection molding of hydrophilic-in-hydrophobic femtolitre-well arrays[J]. Microsystems & Nanoengineering, 5, 25(2019).

    [36] RISSIN D M, WALT D R. Digital readout of target binding with attomole detection limits via enzyme amplification in femtoliter arrays[J]. Journal of the American Chemical Society, 128, 6286-6287(2006).

    [37] RISSIN D M, KAN C W, CAMPBELL T G, et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations[J]. Nature Biotechnology, 28, 595-599(2010).

    [38] LEE J, CRAMPTON K T, TALLARIDA N, et al. Visualizing vibrational normal modes of a single molecule with atomically confined light[J]. Nature, 568, 78-82(2019).

    [39] YERA H, OK V, KUET F L K, et al. PCR and culture for diagnosis of Acanthamoeba keratitis[J]. British Journal of Ophthalmology, 105, 1302-1306(2021).

    [40] HINDSON B J, NESS K D, MASQUELIER D A, et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number[J]. Analytical Chemistry, 83, 8604-8610(2011).

    [41] CHEN Y J, QIAN CH, LIU CH ZH, et al. Nucleic acid amplification free biosensors for pathogen detection[J]. Biosensors and Bioelectronics, 153, 112049(2020).

    [42] GINES G, MENEZES R, NARA K, et al. Isothermal digital detection of microRNAs using background-free molecular circuit[J]. Science Advances, 6, eaay5952(2020).

    [43] COHEN L, HARTMAN M R, AMARDEY-WELLINGTON A, et al. Digital direct detection of microRNAs using single molecule arrays[J]. Nucleic Acids Research, 45, e137(2017).

    [44] ASHTON N J, LEUZY A, KARIKARI T K, et al. The validation status of blood biomarkers of amyloid and phospho-tau assessed with the 5-phase development framework for AD biomarkers[J]. European Journal of Nuclear Medicine and Molecular Imaging, 48, 2140-2156(2021).

    [45] GILL J, LATOUR L, DIAZ-ARRASTIA R, et al. Glial fibrillary acidic protein elevations relate to neuroimaging abnormalities after mild TBI[J]. Neurology, 91, e1385-e1389(2018).

    [46] THELIN E, AL NIMER F, FROSTELL A, et al. A serum protein biomarker panel improves outcome prediction in human traumatic brain injury[J]. Journal of Neurotrauma, 36, 2850-2862(2019).

    [47] PÉREZ-RUIZ E, DECROP D, VEN K, et al. Digital ELISA for the quantification of attomolar concentrations of Alzheimer's disease biomarker protein Tau in biological samples[J]. Analytica Chimica Acta, 1015, 74-81(2018).

    [48] DINH T L, NGAN K C, SHOEMAKER C B, et al. Rapid and ultrasensitive detection of botulinum neurotoxin serotype A1 in human serum and urine using single-molecule array method[J]. Forensic Toxicology, 35, 179-184(2017).

    [49] WANG X, COHEN L, WANG J, et al. Competitive immunoassays for the detection of small molecules using single molecule arrays[J]. Journal of the American Chemical Society, 140, 18132-18139(2018).

    [50] KIM E, BAASKE M D, VOLLMER F. Towards next-generation label-free biosensors: recent advances in whispering gallery mode sensors[J]. Lab on a Chip, 17, 1190-1205(2017).

    [51] SUBRAMANIAN S, VINCENT S, VOLLMER F. Effective linewidth shifts in single-molecule detection using optical whispering gallery modes[J]. Applied Physics Letters, 117, 151106(2020).

    [52] SANTIAGO-CORDOBA M A, CETINKAYA M, BORISKINA S V, et al. Ultrasensitive detection of a protein by optical trapping in a photonic-plasmonic microcavity[J]. Journal of Biophotonics, 5, 629-638(2012).

    [53] YU W Y, JIANG W C, LIN Q, et al. Cavity optomechanical spring sensing of single molecules[J]. Nature Communications, 7, 12311(2016).

    [54] BAILEY R C, WASHBURN A L, QAVI A J, et al. A robust silicon photonic platform for multiparameter biological analysis[J]. Proceedings of SPIE, 7220, 72200N(2009).

    [55] SHI H X, CUI J J, SULEMANA H, et al. Protein detection based on rolling circle amplification sensors[J]. Luminescence, 36, 842-848(2021).

    [56] NITU F R, SAVU L, MURARU S, et al. Label-free homogeneous microRNA detection in cell culture medium based on graphene oxide and specific fluorescence quenching[J]. Nanomaterials, 11, 368(2021).

    [57] VOLLMER F, ARNOLD S, KENG D. Single virus detection from the reactive shift of a whispering-gallery mode[J]. Proceedings of the National Academy of Sciences of the United States of America, 105, 20701-20704(2008).

    [58] CARDENOSA-RUBIO M C, ROBISON H M, BAILEY R C. Recent advances in environmental and clinical analysis using microring resonator–based sensors[J]. Current Opinion in Environmental Science & Health, 10, 38-46(2019).

    [59] SHAO L B, JIANG X F, YU X CH, et al. Detection of single nanoparticles and lentiviruses using microcavity resonance broadening[J]. Advanced Materials, 25, 5616-5620(2013).

    [60] DOMINGUEZ I, DEL VILLAR I, FUENTES O, et al. Dually nanocoated planar waveguides towards multi-parameter sensing[J]. Scientific Reports, 11, 3669(2021).

    [61] COGNETTI J S, STEINER D J, ABEDIN M, et al. Disposable photonics for cost-effective clinical bioassays: application to COVID-19 antibody testing[J]. Lab on a Chip, 21, 2913-2921(2021).

    [62] ROBISON H M, ESCALANTE P, VALERA E, et al. Precision immunoprofiling to reveal diagnostic signatures for latent tuberculosis infection and reactivation risk stratification[J]. Integrative Biology, 11, 16-25(2019).

    [63] YU X CH, TANG SH J, LIU W J, et al. Single-molecule optofluidic microsensor with interface whispering gallery modes[J]. Proceedings of the National Academy of Sciences of the United States of America, 119, e2108678119(2022).

    [64] KIM E, BAASKE M D, VOLLMER F. In situ observation of single-molecule surface reactions from low to high affinities[J]. Advanced Materials, 28, 9941-9948(2016).

    [65] KIM E, BAASKE M D, SCHULDES I, et al. Label-free optical detection of single enzyme-reactant reactions and associated conformational changes[J]. Science Advances, 3, e1603044(2017).

    [66] SUBRAMANIAN S, JONES H B L, FRUSTACI S, et al. Sensing enzyme activation heat capacity at the single-molecule level using gold-nanorod-based optical whispering gallery modes[J]. ACS Applied Nano Materials, 4, 4576-4583(2021).

    [67] AMBARTSUMYAN O, GRIBANYOV D, KUKUSHKIN V, et al. SERS-based biosensors for virus determination with oligonucleotides as recognition elements[J]. International Journal of Molecular Sciences, 21, 3373(2020).

    [68] FLEISCHMANN M, HENDRA P J, MCQUILLAN A J. Raman spectra of pyridine adsorbed at a silver electrode[J]. Chemical Physics Letters, 26, 163-166(1974).

    [69] LI W Y, CAMARGO P H C, LU X M, et al. Dimers of silver nanospheres: facile synthesis and their use as hot spots for surface-enhanced Raman scattering[J]. Nano Letters, 9, 485-490(2009).

    [70] BLACKIE E J, LE RU E C, ETCHEGOIN P G. Single-molecule surface-enhanced Raman spectroscopy of nonresonant molecules[J]. Journal of the American Chemical Society, 131, 14466-14472(2009).

    [71] LINDQUIST N C, DE ALBUQUERQUE C D L, SOBRAL-FILHO R G, et al. High-speed imaging of surface-enhanced Raman scattering fluctuations from individual nanoparticles[J]. Nature Nanotechnology, 14, 981-987(2019).

    [72] LI ZH Y. Mesoscopic and microscopic strategies for engineering Plasmon-enhanced Raman scattering[J]. Advanced Optical Materials, 6, 1701097(2018).

    [73] YAMPOLSKY S, FISHMAN D A, DEY S, et al. Seeing a single molecule vibrate through time-resolved coherent anti-Stokes Raman scattering[J]. Nature Photonics, 8, 650-656(2014).

    [74] ZHANG K, LIU Y J, WANG Y N, et al. Direct SERS tracking of a chemical reaction at a single 13 nm gold nanoparticle[J]. Chemical Science, 10, 1741-1745(2019).

    [75] NASIR S, MAJEED M I, NAWAZ H, et al. Surface enhanced Raman spectroscopy of RNA samples extracted from blood of hepatitis C patients for quantification of viral loads[J]. Photodiagnosis and Photodynamic Therapy, 33, 102152(2021).

    [76] CHEN H, PARK S G, CHOI N, et al. SERS imaging-based aptasensor for ultrasensitive and reproducible detection of influenza virus A[J]. Biosensors and Bioelectronics, 167, 112496(2020).

    [77] CHAUHAN N, SAXENA K, TIKADAR M, et al. Recent advances in the design of biosensors based on novel nanomaterials: an insight[J]. Nanotechnology and Precision Engineering, 4, 045003(2021).

    [78] NGUYEN H A, JUPIN I, DECORSE P, et al. Assembly of gold nanoparticles using turnip yellow mosaic virus as an in-solution SERS sensor[J]. RSC Advances, 9, 32296-32307(2019).

    [79] KUKUSHKIN V I, IVANOV N M, NOVOSELTSEVA A A, et al. Highly sensitive detection of influenza virus with SERS aptasensor[J]. PLoS One, 14, e0216247(2019).

    [80] PENG Y S, LIN C L, LONG L, et al. Charge-transfer resonance and electromagnetic enhancement synergistically enabling MXenes with excellent SERS sensitivity for SARS-CoV-2 S protein detection[J]. Nano-Micro Letters, 13, 52(2021).

    [81] ANTOINE D, MOHAMMADI M, VITT M, et al. Rapid, point-of-care scFv-SERS assay for femtogram level detection of SARS-CoV-2[J]. ACS Sensors, 7, 866-873(2022).

    [82] LIU B, ZHENG SH Y, LI H T, et al. Ultrasensitive and facile detection of multiple trace antibiotics with magnetic nanoparticles and core-shell nanostar SERS nanotags[J]. Talanta, 237, 122955(2022).

    [83] SHIN H, OH S, KANG D, et al. Protein quantification and imaging by surface-enhanced Raman spectroscopy and similarity analysis[J]. Advanced Science, 7, 1903638(2020).

    [84] ZHOU W, TIAN Y F, YIN B CH, et al. Simultaneous surface-enhanced Raman spectroscopy detection of multiplexed microRNA biomarkers[J]. Analytical Chemistry, 89, 6120-6128(2017).

    [85] PANG Y F, WANG CH G, LU L CH, et al. Dual-SERS biosensor for one-step detection of microRNAs in exosome and residual plasma of blood samples for diagnosing pancreatic cancer[J]. Biosensors and Bioelectronics, 130, 204-213(2019).

    [86] NING C F, WANG L Y, TIAN Y F, et al. Multiple and sensitive SERS detection of cancer-related exosomes based on gold–silver bimetallic nanotrepangs[J]. Analyst, 145, 2795-2804(2020).

    [87] LI L, LIU CH, CAO X W, et al. Multiplexing determination of cancer-associated biomarkers by surface-enhanced Raman scattering using ordered gold nanohoneycomb arrays[J]. Bioanalysis, 9, 1561-1572(2017).

    [88] ATANASOV A G, ZOTCHEV S B, DIRSCH V M, et al. Natural products in drug discovery: advances and opportunities[J]. Nature Reviews Drug Discovery, 20, 200-216(2021).

    [89] CARTER L J, GARNER L V, SMOOT J W, et al. Assay techniques and test development for COVID-19 diagnosis[J]. ACS Central Science, 6, 591-605(2020).

    [90] DE PUIG H, LEE R A, NAJJAR D, et al. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants[J]. Science Advances, 7, eabh2944(2021).

    [91] MYHRVOLD C, FREIJE C A, GOOTENBERG J S, et al. Field-deployable viral diagnostics using CRISPR-Cas13[J]. Science, 360, 444-448(2018).

    [92] GOOTENBERG J S, ABUDAYYEH O O, KELLNER M J, et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6[J]. Science, 360, 439-444(2018).

    [93] MAKAROVA K S, WOLF Y I, IRANZO J, et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants[J]. Nature Reviews Microbiology, 18, 67-83(2020).

    CLP Journals

    [1] Jing LU, Wei-xing LI, Xiao-jun XU, Wei JI. Recent development of cryo-correlated light and electron microscopy[J]. Chinese Optics, 2022, 15(6): 1275

    Tools

    Get Citation

    Copy Citation Text

    Wen-chao ZHOU, Zheng-hao LI, Jie WU. Research progress of single molecule biological detection methods and applications[J]. Chinese Optics, 2022, 15(5): 878

    Download Citation

    EndNote(RIS)BibTexPlain Text
    Save article for my favorites
    Paper Information

    Category: Review

    Received: Jun. 14, 2022

    Accepted: --

    Published Online: Sep. 29, 2022

    The Author Email:

    DOI:10.37188/CO.2022-0129

    Topics