Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy

Lei Jin; Li Kou; Yanan Zeng; Chunguang Hu; Xiaodong Hu

doi:10.1007/s41048-019-00097-4

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Article Navigation > Biophysics Reports > 2019 > 5(4): 176-183

Lei Jin, Li Kou, Yanan Zeng, Chunguang Hu, Xiaodong Hu. Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy. Biophysics Reports, 2019, 5(4): 176-183. doi: 10.1007/s41048-019-00097-4

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Lei Jin, Li Kou, Yanan Zeng, Chunguang Hu, Xiaodong Hu. Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy. Biophysics Reports, 2019, 5(4): 176-183. doi: 10.1007/s41048-019-00097-4

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Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy

doi: 10.1007/s41048-019-00097-4

Lei Jin^1,3,
Li Kou^1,3,
Yanan Zeng²,
Chunguang Hu^1,3,
Xiaodong Hu^{1,3
,
,}

1 State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
2 College of Engineering and Technology, Tianjin Agricultural University, Tianjin 300384, China
3 Nanchang Institute for Microtechnology of Tianjin University, Tianjin 300072, China

Funds: This work was financially supported by the National Nature Science Foundation of China (51775381), National Major Scientific Instruments and Equipment Development Special (2017YFF0107001), and The Tianjin Research Program of Application Foundation and Advanced Technology (15JCZDJC3160).

More Information

Corresponding author: Xiaodong Hu
Received Date: 28 November 2018
Publish Date: 31 August 2019

Abstract

Abstract

Inefficient sample preparation methods hinder the performance of high-throughput single-molecule force spectroscopy (H-SMFS) for viscous damping among reactants and unstable linkage. Here, we demonstrated a sample preparation method for H-SMFS systems to achieve a higher ratio of effective target molecules per sample cell by gas-phase silanization and reactant hydrophobization. Digital holographic centrifugal force microscopy (DH-CFM) was used to verify its performance. The experimental result indicated that the DNA stretching success ratio was improved from 0.89% to 13.5%. This enhanced efficiency preparation method has potential application for force-based DNA stretching experiments and other modifying procedures.

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References(29)

References

Abels JA, Moreno-Herrero F, Van der Heijden T, Dekker C, Dekker NH (2005) Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J 88:2737-2744

Bennink ML, Schärer OD, Kanaar R, Sakata-Sogawa K, Schins JM, Kanger JS, de Grooth BG, Greve J (1999) Single-molecule manipulation of double-stranded DNA using optical tweezers:interaction studies of DNA with RecA and YOYO-1. Cytometry 36:200-208

Di X, Zhang W, Zang D, Liu F, Wang Y, Wang C (2016) A novel method for the fabrication of superhydrophobic nylon net.Chem Eng J 306:53-59

Fan C, Lopinski G (2010) STM and HREELS investigation of gas phase silanization on hydroxylated Si (100). Surf Sci 604:996-1001

Halvorsen K, Wong WP (2010) Massively parallel single-molecule manipulation using centrifugal force. Biophys J 98:L53-L55

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

Hill FR, Monachino E, van Oijen AM (2017) The more the merrier:high-throughput single-molecule techniques. Biochem Soc Trans 45:759-769

Hoang T, Patel DS, Halvorsen K (2016) A wireless centrifuge force microscope (CFM) enables multiplexed single-molecule experiments in a commercial centrifuge. Rev Sci Instrum 87:083705

Johnson KC, Clemmens E, Mahmoud H, Kirkpatrick R, Vizcarra JC, Thomas WE (2017) A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control.J Biol Eng 11:47

Kango S, Kalia S, Celli A, Njuguna J, Habibi Y, Kumar R (2013)Surface modification of inorganic nanoparticles for development of organic-inorganic nanocomposites-a review. Prog Polym Sci 38:1232-1261

Kirby BJ (2010) Micro-and nanoscale fluid mechanics:transport in microfluidic devices. Cambridge University Press, Cambridge Kreft D, Wang Y, Rattay M, Toensing K, Anselmetti D (2018)

Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers.J Nanobiotechnol 16:56

Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J (2017) Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res 45:5920-5929

Kriegel F, Vanderlinden W, Nicolaus T, Kardinal A, Lipfert J (2018)Measuring single-molecule twist and torque in multiplexed magnetic tweezers. Methods Mol Biol 1814:75-98

Kwak K, Kudo H, Fujihira M (2003a) Imaging stretched single DNA molecules by pulsed-force-mode atomic force microscopy.Ultramicroscopy 97:249-255

Kwak K, Yoda S, Fujihira M (2003b) Observation of stretched single DNA molecules by Kelvin probe force microscopy. Appl Surf Sci 210:73-78

Kwak K, Sato F, Kudo H, Yoda S, Fujihira M (2004) Topographic effects on adhesive force mapping of stretched DNA molecules by pulsed-force-mode atomic force microscopy. Ultramicroscopy 100:179-186

Lipfert J, Kerssemakers JWJ, Jager T, Dekker NH (2010) Magnetic torque tweezers:measuring torsional stiffness in DNA and RecA-DNA filaments. Nat Methods 7:977-980

Lu X, Soto F, Li J, Li T, Liang Y, Wang J (2017) Topographical manipulation of microparticles and cells with acoustic microstreaming. ACS Appl Mater Interfaces 9:38870-38876

Lung CYK, Matinlinna JP (2012) Aspects of silane coupling agents and surface conditioning in dentistry:an overview. Dent Mater 28:467-477

Madariaga-Marcos J, Hormeño S, Pastrana C, Fisher G, Dillingham M, Moreno-Herrero F (2018) Force determination in lateral magnetic tweezers combined with TIRF microscopy.Nanoscale 10:4579-4590

Neuman KC, Nagy A (2008) Single-molecule force spectroscopy:optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5:491

Pan C, Kou K, Jia Q, Zhang Y, Wu G, Ji T (2017) Improved thermal conductivity and dielectric properties of hBN/PTFE composites via surface treatment by silane coupling agent. Compos B Eng 111:83-90

Shi H, He Y, Pan Y, Di H, Zeng G, Zhang L, Zhang C (2016) A modified mussel-inspired method to fabricate TiO₂ decorated superhydrophilic PVDF membrane for oil/water separation.J Membr Sci 506:60-70

Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA:the elastic response of individual double-stranded and singlestranded DNA molecules. Science 271:795-799

Steinbach AM, Sandner T, Mizaikoff B, Strehle S (2016) Gas phase silanization for silicon nanowire sensors and other lab-on-achip systems. Physica Status Solidi (c) 13:135-141

Xie Y, Hill CA, Xiao Z, Militz H, Mai C (2010) Silane coupling agents used for natural fiber/polymer composites:a review. Compos Part A 41:806-819

Yang D, Ward A, Halvorsen K, Wong WP (2016) Multiplexed singlemolecule force spectroscopy using a centrifuge. Nat Commun 7:11026

Yokokawa R, Miwa J, Tarhan MC, Fujita H, Kasahara M (2008) DNA molecule manipulation by motor proteins for analysis at the single-molecule level. Anal Bioanal Chem 391:2735

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