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The functions of DNA-binding proteins are dependent on protein-induced DNA distortion, the binding preference to special sequences, DNA secondary structures, the binding kinetics and the binding affinity. Recent rapid progress in single-molecule imaging and mechanical manipulation technologies have made it possible to directly probe the DNA binding by proteins, footprint the positions of the bound proteins on DNA, quantify the kinetics and the affinity of protein–DNA interactions, and study the interplay of protein binding with DNA conformation and DNA topology. Here, we review the applications of an integrated approach where the single-DNA imaging using atomic force microscopy and the mechanical manipulation of single DNA molecules are combined to study the DNA–protein interactions. We also provide our views on how these findings yield new insights into understanding the roles of several essential DNA architectural proteins.
Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181(20): 6361−6370
Amit R, Oppenheim AB, Stavans J (2003) Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor. Biophys J 84(4): 2467−2473
Arold ST, Leonard PG, Parkinson GN, Ladbury JE (2010) H-NS forms a superhelical protein scaffold for DNA condensation. Proc Natl Acad Sci USA 107(36): 15728−15732
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3): 381−395
Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, Koster AJ, Woodcock CL (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA 95(24): 14173−14178
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, 3rd, Bulyk ML (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24(11): 1429−1435
Bianchi ME, Agresti A (2005) HMG proteins: dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 15(5): 496−506
Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56(9): 930−933
Blank TA, Becker PB (1996) The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing. J Mol Biol 260(1): 1−8
Bouffartigues E, Buckle M, Badaut C, Travers A, Rimsky S (2007) H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat Struct Mol Biol 14(5): 441−448
Brent Brower-Toland MDW (2004) Use of optical trapping techniques to study single-nucleosome dynamics. Methods Enzymol 376: 62−72
Browning DF, Grainger DC, Busby SJ (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13(6): 773−780
Bustin M (1999) Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol Cell Biol 19(8): 5237−5246
Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E (2004) DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res 32(19): 5935−5944
Dame RT (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 56(4): 858−870
Dame RT, Wyman C, Goosen N (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28(18): 3504−3510
Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8(3): 185−195
Dufrene YF, Ando T, Garcia R, Alsteens D, Martinez-Martin D, Engel A, Gerber C, Muller DJ (2017) Imaging modes of atomic force microscopy for application in molecular and cell biology. Nat Nanotechnol 12(4): 295−307
Fagerstam LG, Frostell-Karlsson A, Karlsson R, Persson B, Ronnberg I (1992) Biospecific interaction analysis using surface plasmon resonance detection applied to kinetic, binding site and concentration analysis. J Chromatogr 597(1-2): 397−410
Fried M, Crothers DM (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9(23): 6505−6525
Fu H, Freedman BS, Lim CT, Heald R, Yan J (2011) Atomic force microscope imaging of chromatin assembled in Xenopus laevis egg extract. Chromosoma 120(3): 245−254
Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5(9): 3157−3170
Gao Y, Foo YH, Winardhi RS, Tang Q, Yan J, Kenney LJ (2017) Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells. Proc Natl Acad Sci USA 114(47): 12560−12565
Gerber C, Lang HP (2006) How the doors to the nanoworld were opened. Nat Nanotechnol 1(1): 3−5
Germond JE, Hirt B, Oudet P, Gross-Bellark M, Chambon P (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci USA 72(5): 1843−1847
Goodman FO, Garcia N (1991) Roles of the attractive and repulsive forces in atomic-force microscopy. Phys Rev B Condens Matter 43(6): 4728−4731
Goosen N, van de Putte P (1995) The regulation of transcription initiation by integration host factor. Mol Microbiol 16(1): 1−7
Gulvady R, Gao Y, Kenney LJ, Yan J (2018) A single molecule analysis of H-NS uncouples DNA binding affinity from DNA specificity. Nucleic Acids Res 46(19): 10216−10224
Hales LM, Gumport RI, Gardner JF (1994) Determining the DNA sequence elements required for binding integration host factor to two different target sites. J Bacteriol 176(10): 2999−3006
Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, Wang MD (2009) High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol 16(2): 124−129
Hansma HG, Laney DE, Bezanilla M, Sinsheimer RL, Hansma PK (1995) Applications for atomic force microscopy of DNA. Biophys J 68(5): 1672−1677
Hinterdorfer P, Dufrene YF (2006) Detection and localization of single molecular recognition events using atomic force microscopy. Nat Methods 3(5): 347−355
Jameson DM, Ross JA (2010) Fluorescence polarization/anisotropy in diagnostics and imaging. Chem Rev 110(5): 2685−2708
Kaczmarczyk A, Brouwer TB, Pham C, Dekker NH, van Noort J (2018) Probing chromatin structure with magnetic tweezers. Methods Mol Biol 1814: 297−323
Kaczmarczyk A, Meng H, Ordu O, Noort JV, Dekker NH (2020) Chromatin fibers stabilize nucleosomes under torsional stress. Nat Commun 11(1): 126. https://doi.org/10.1038/s41467-019-13891-y
Koch SJ, Shundrovsky A, Jantzen BC, Wang MD (2002) Probing protein-DNA interactions by unzipping a single DNA double helix. Biophys J 83(2): 1098−1105
Kornberg RD (1977) Structure of chromatin. Annu Rev Biochem 46: 931−954
Kruithof M, Chien FT, Routh A, Logie C, Rhodes D, van Noort J (2009) Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nat Struct Mol Biol 16(5): 534−540
Kruithof M, van Noort J (2009) Hidden Markov analysis of nucleosome unwrapping under force. Biophys J 96(9): 3708−3715
Krzemien KM, Beckers M, Quack S, Michaelis J (2017) Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution. PLoS one 12(3): e0173459. https://doi.org/10.1371/journal.pone.0173459
Lang B, Blot N, Bouffartigues E, Buckle M, Geertz M, Gualerzi CO, Mavathur R, Muskhelishvili G, Pon CL, Rimsky S, Stella S, Babu MM, Travers A (2007) High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res 35(18): 6330−6337
Le S, Chen H, Cong P, Lin J, Droge P, Yan J (2013) Mechanosensing of DNA bending in a single specific protein-DNA complex. Sci Rep 3: 3508. https://doi.org/10.1038/srep03508
Lee SY, Lim CJ, Droge P, Yan J (2015) Regulation of bacterial DNA packaging in early stationary phase by competitive DNA binding of Dps and IHF. Sci Rep 5: 18146. https://doi.org/10.1038/srep18146
Li W, Chen P, Yu J, Dong L, Liang D, Feng J, Yan J, Wang P-Y, Li Q, Zhang Z, Li M, Li G (2016) FACT remodels the tetranucleosomal unit of chromatin fibers for gene transcription. Molecular Cell 64(1): 120−133
Liang L, Ma K, Wang Z, Janissen R, Yu Z (2021) Dynamics and inhibition of MLL1 CXXC domain on DNA revealed by single-molecule quantification. Biophys J 120(16): 3283−3291
Lim CJ, Lee SY, Kenney LJ, Yan J (2012a) Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing. Sci Rep 2: 509. https://doi.org/10.1038/srep00509
Lim CJ, Whang YR, Kenney LJ, Yan J (2012b) Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility. Nucleic Acids Res 40(8): 3316−3328
Lipfert J, Wiggin M, Kerssemakers JW, Pedaci F, Dekker NH (2011) Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids. Nat Commun 2: 439. https://doi.org/10.1038/ncomms1450
Liu Y, Chen H, Kenney LJ, Yan J (2010) A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes. Genes Dev 24(4): 339−344
Luijsterburg MS, Noom MC, Wuite GJ, Dame RT (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156(2): 262−272
Luijsterburg MS, White MF, van Driel R, Dame RT (2008) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43(6): 393−418
Manosas M, Camunas-Soler J, Croquette V, Ritort F (2017) Single molecule high-throughput footprinting of small and large DNA ligands. Nat Commun 8(1): 304. https://doi.org/10.1038/s41467-017-00379-w
Mihardja S, Spakowitz AJ, Zhang Y, Bustamante C (2006) Effect of force on mononucleosomal dynamics. Proc Natl Acad Sci USA 103(43): 15871−15876
Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6): 491−505
Ngo TT, Zhang Q, Zhou R, Yodh JG, Ha T (2015) Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. Cell 160(6): 1135−1144
Norton VG, Imai BS, Yau P, Bradbury EM (1989) Histone acetylation reduces nucleosome core particle linking number change. Cell 57(3): 449−457
Ozturk N, Singh I, Mehta A, Braun T, Barreto G (2014) HMGA proteins as modulators of chromatin structure during transcriptional activation. Front Cell Dev Biol 2: 5. https://doi.org/10.3389/fcell.2014.00005
Poirier MG, Bussiek M, Langowski J, Widom J (2008) Spontaneous access to DNA Target sites in folded chromatin fibers. J Mol Biol 379(4): 772−786
Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee AS, Luscombe NM (2012) Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res 40(8): 3524−3537
Reeves R (2010) Nuclear functions of the HMG proteins. Biochim Biophys Acta 1799(1-2): 3−14
Renault M, Garcia J, Cordeiro TN, Baldus M, Pons M (2013) Protein oligomers studied by solid-state NMR-the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein. FEBS J 280(12): 2916−2928
Rice PA, Yang S, Mizuuchi K, Nash HA (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87(7): 1295−1306
Royer CA, Scarlata SF (2008) Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol 450: 79−106
Simpson RT, Thoma F, Brubaker JM (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell 42(3): 799−808
Spurio R, Durrenberger M, Falconi M, La Teana A, Pon CL, Gualerzi CO (1992) Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy. Mol Gen Genet 231(2): 201−211
van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT (2004) Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci USA 101(18): 6969−6974
Vlijm R, Lee M, Lipfert J, Lusser A, Dekker C, Dekker NH (2015) Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell Rep 10(2): 216−225
Vlijm R, Smitshuijzen JS, Lusser A, Dekker C (2012) NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers. PLoS One 7(9): e46306. https://doi.org/10.1371/journal.pone.0046306
Wang H, Bash R, Yodh JG, Hager GL, Lohr D, Lindsay SM (2002) Glutaraldehyde modified mica: a new surface for atomic force microscopy of chromatin. Biophys J 83(6): 3619−3625
Wang Y, Yan J, Goult BT (2019) Force-dependent binding constants. Biochemistry 58(47): 4696−4709
Weber G (1952) Polarization of the fluorescence of macromolecules. I. Theory and experimental method. Biochem J 51(2): 145−155
Widom J (1989) Toward a unified model of chromatin folding. Annu Rev Biophys Biophys Chem 18: 365−395
Winardhi RS, Castang S, Dove SL, Yan J (2014) Single-molecule study on histone-like nucleoid-structuring protein (H-NS) paralogue in Pseudomonas aeruginosa: MvaU bears DNA organization mode similarities to MvaT. PLoS One 9(11): e112246. https://doi.org/10.1371/journal.pone.0112246
Winardhi RS, Fu W, Castang S, Li Y, Dove SL, Yan J (2012) Higher order oligomerization is required for H-NS family member MvaT to form gene-silencing nucleoprotein filament. Nucleic Acids Res 40(18): 8942−8952
Winardhi RS, Yan J, Kenney LJ (2015) H-NS regulates gene expression and compacts the nucleoid: insights from single-molecule experiments. Biophys J 109(7): 1321−1329
Woodcock CL, Dimitrov S (2001) Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 11(2): 130−135
Yan J, Maresca TJ, Skoko D, Adams CD, Xiao B, Christensen MO, Heald R, Marko JF (2007) Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics. Mol Biol Cell 18(2): 464−474
Yoshua SB, Watson GD, Howard JAL, Velasco-Berrelleza V, Leake MC, Noy A (2021) Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity. Nucleic Acids Res 49(15): 8684−8698
Yu H, Lim HH, Tjokro NO, Sathiyanathan P, Natarajan S, Chew TW, Klonisch T, Goodman SD, Surana U, Droge P (2014) Chaperoning HMGA2 protein protects stalled replication forks in stem and cancer cells. Cell Rep 6(4): 684−697
Zhao X, Guo S, Lu C, Chen J, Le S, Fu H, Yan J (2019) Single-molecule manipulation quantification of site-specific DNA binding. Curr Opin Chem Biol 53: 106−117
Zhao X, Peter S, Droge P, Yan J (2017) Oncofetal HMGA2 effectively curbs unconstrained (+) and (-) DNA supercoiling. Sci Rep 7(1): 8440. https://doi.org/10.1038/s41598-017-09104-5
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