• Nucleic Acids

    SPM Applications in Biology

    Nucleic Acids

    Nucleic acids, especially RNA and DNA, are being extensively investigated since the very beginning of AFM. To show the variety of studies in this field we summarized the results and details of sample preparation in the table below. The material from sources in this table is taken from an extended review by Prof. A. Ikai [ 256 ] with the permission of the author and publisher.

    ID What was studied Details of sample preparation
    1506 Nucleosomal DNA with 146 nucleotide base pairs. Both aggregates and individual molecules with lengths corresponding to theoretical values of 52 nm were discerned Electrochemical deposition
    15 mer DNA of solely pyrimidine bases  
    1510 Circular plasmid DNA and 623 base pair fSK14 restriction fragments. First recipe: Deposition of DNA on an untreated mica surface followed by first blotting, then washing in an ammonium acetate solution, and finally air drying before scanning in AFM
    Second recipe: Heating the washed sample to 80°C for 30 - 60 min in a vacuum oven before imaging since DNA molecules after heating is much more stable against scanning compared with air dried ones.
    1511 Nanodissection of supercoiled plasmid DNA. A part of 100 - 150 nm in length consisting of 300 - 400 base pairs was excised (it was stated that it is a much shorter fragment of DNA than that of cut using a glass needle and a micromanipulator).  
    1529 The effects of adhesion and scanning force were examined on DNA and a linear fd phage. The width and height of DNAs in the images taken under various environmental conditions were carefully measured. Authors concluded that the AFM image resolution depended more on the adhesion than the force exerted by the tip on samples.  
    1532 Double stranded renovirus genome DNA of 10 nm or more in width  
    1534 Two DNA complexes:
    1) Cytochrome c:DNA
    2) DNA:polymerase
    1) Cytochrome c was added to DNA in solution
    2) The Klenow fragment of DNA polymerase I was added together with dNTP to start a random priming reaction
    1536 Circular plasmid DNA strings of 8 nm in width Incubating in aqueous DNA solutions at 35°C.
    1542 Binding of RNA polymrase on DNA as a transcription complex was studied. 681 bp fragments of DNA containing lPL promotor and E.coli RNA polymerase were used. DNA appeared bent (about 54°) in an open promotor complex containing RNA polymerase and more severely bent in an elongation complex (average 92°) where the enzyme completed RNA synthesis up to 15 nucleotides.  
    1543 DNA was imaged wider and higher (about twice) in aqueous environment than in propanol presumably because the AFM tip was imaging hydration layers around DNA, according to the authors. DNA was extensively dehydrated by baking in vacuum before being transferred to an aqueous environment containing MgCl2.
    1544 DNA was imaged with an expected length for B-DNA, its width being thinner at the two ends where it was anchored to the substrate and wider in the middle, which, the authors believed, allowed the freedom for DNA molecules to react with other molecules such as enzymes. The result in propanol was better in the sense that DNA was imaged thinner than in water and the substrate surface was clean. Inclusion of dithiothreitol (DTT) in DNA solution was necessary to disaggregate DNA. DNA of a specific length was PCR amplified (see the paper for details). The amplified double helical DNA fragments were thiolated at both ends. An aqueous solution of thiolated DNA was applied on a gold-coated mica surface for 40 - 60 min and dried without blotting so that the number density of chemisorbed DNA could be increased. The dried sample was washed to remove free DNA and submerged in either an aqueous salt solution containing dithiothreitol (DTT) or in propanol for AFM imaging.
    1545 High quality images of DNA with excellent resolution revealing a periodic corrugation along a DNA strand with repeats corresponding to the double helical structure of DNA are presented.  
    1546 Binding dynamics of the E.coli RNA polymerase complex to a short fragment of DNA of 1258 base pairs that contained lPR promotor was studied. A binding-unbinding-rebinding process of RNA polymerase complex on a single piece of DNA imaged at roughly every 70 s. DNA in a buffer containing 1 mM MgCl2 was deposited on freshly cleaved ruby mica for 10 s and washed thoroughly with clean water. The sample was then dried under nitrogen and put in a desiccator. It was then placed in a liquid cell and scanned with a contact mode AFM
    1547 A plasmid DNA was imaged with good reproducibility and its width was as small as 3 nm. Occasionally some reproducible bumps were observed along the double helical strand of DNA and they were tentatively interpreted as representing a feature associated with the double helical nature of DNA. DNA was deposited onto mica surface from a solution containing MgCl2 and, after drying, immersed under either n-propanol, n-butanol or isopropanol.
    1548 Contact mode imaging of DNA labeled with gold particle and attached to a mica surface were performed. The height of nominally 5 nm gold spheres was estimated as 5.8 ± 0.12 nm from the image and that of DNA was 0.54 ± 0.12 nm in air of relative humidity less than 10 %. DNA labeled with a spherical gold particle at one end and deposited on the mica surface was dried with nitrogen. It allowed a more stable imaging of DNA than with an unlabeled DNA since gold sphere at the end of DNA stuck to the mica substrate rather firmly.
    1549 The location of the binding protein (Ferric uptake repression protein, Fur repressor) on DNA was studied by Electron Microscopy and AFM. No bend in the DNA structure were observed after Fur binding. The repressor protein bound on DNA had a shape like a peanut shell with two globular domains. The domain structure was clearer in the AFM image than in the dark field TEM image of a metal coated sample.  
    1550 A class of compounds with a capability of binding to DNA and straightening it were studied. The AFM images of kinetoplast DNA with and without distamycin or MGT-6b showed a distinct difference in the shape of the samples.  
    1551 A dynamic process of degradation of DNA in the presence of Dnase I, an enzyme that hydrolyzes phosphodiester bonds of DNA without requirement for specific base sequences was studied. After an AFM scan was started in a tapping mode for imaging of DNA, Dnase I was added to the DNA solution and progressive splitting and degradation of DNA were continuously monitored with repeated scans. A double stranded DNA was adsorbed on a mica surface that was treated with NiCl2 prior to application of a solution containing DNA and the loosely adsorbed DNAs were washed off with high pressure water.
    Z-DNA and G-wire DNA have been treated. Z-DNA was biochemically identified by using a specific antibody. The antibody was imaged as a globular protrusion at a fixed position in a linear DNA molecule. G-wire DNA is a member of the quadruple helical nucleic acid family and its structure was imaged clearly with AFM. Z-DNA was inserted as a d(CG)11 fragment into pAN022 DNA plasmid.

    It is very important to find out the best substrate for imaging biological objects since both tight and almost loose bonding to the substrate does not allow for the best scanning conditions. To a great extent it concerns DNA and RNA imaging. Apart from freshly cleaved mica a number of substrates or methods to anchor DNA or RNA to this substrates were proposed: mica surface pretreated with cadmium arachidate and coated with LB film [1507, 1508], mica surface modified with 3-aminophopyltriethoxy silane (APTES) [1532], mica surface treated with NiCl2 [1551], etc. It was shown, for example, that the supercoiled structure of DNA can be imaged directly only using a mica substrate treated with spermine but not the freshly cleaved mica or APTES-mica [384]. Mou at al. [523] found that a cationic lipid bilayer is an excellent support for DNA anchoring due to the relatively strong electrostatic interaction between the DNA phosphate groups and the positively charged lipid headgroups. Using AFM they obtained reproducible images of double stranded DNA helix and measured its period with a high accuracy of 3,4 ± 0,4 nm which is in an excellent agreement with the known pitch of the dsDNA. Refer to a paper of P. Wagner [1024] for summary on immobilization techniques for SPM.

    One of the most interesting DNA related phenomenon is its supercoiling mentioned above. Supercoiling is the object of investigation in many studies [384, 560, 1000, 1119, 1124]. Atomic force microscopy has always contributed significantly to the understanding of this phenomenon and has proved to be preferable among other powerful direct imaging methods such as electron microscopy mainly due to the natural physiological conditions of DNA imaging.

    Stevenson et al. [1622] reported fabrication of DNA biosensor on the AFM microcantilever platform. In their study, gold-coated rectangular cantilevers (MikroMasch) were functionalized with double-stranded thiolated DNA and exposed to a reaction buffer without and then with the small reducing agent DTT (dithiothreitol). Significant cantilever deflection occurred upon exposure to the buffer containing DTT indicating either reaction of the DTT on the gold side (at interstitial locations) or exchange of immobilized DNA for DTT.

    Radiation is considered one of the main causes of cell inactivation due to the damage of DNA. Until recently the consequences of such damaging were studied with various other methods but not with AFM. However, now AFM is becoming a powerful tool in radiation biological research. Murakami at al [321] report on nanometer-level-structure analysis of DNA damage. Three forms of plasmid DNA, closed circular (intact DNA), open circular (DNA with a single strand break) and linear form (DNA with a double strand break) were visualized after g-irradiation. Authors stressed that the torsional feature of the plasmid DNA was imaged better with AFM than with a transmission electron microscope (TEM) and structural changes of DNA were discernible by AFM with nanoscale resolution. See also the latest paper on DNA and chromosome irradiation effect [708].

    The prospects that have seemed science fiction a decade ago are now coming true little by little. For example, researchers from IBM reported on the attempts to make AFM based sensor for identifying gene mutations [1589]. DNA strands immobilized on a cantilever surface react in specific way dependent upon the match or mismatch of the complementary strands of DNA in a solution. The heat evolved upon a match forces the cantilever to bend.

    Finally, several tasks can be listed that have been successfully solved with the help of AFM: high resolution imaging of DNA [523, 652, 1588] and synthesized nucleic acids [1557], investigation of DNA stiffness or elasticity [790, 996, 1586, 1587], segmental dynamics of DNA [1119], [1306], processes of gene transfection [354] and recovering DNA from biological samples [684].

    It is hard to attend to every paper in the huge amount of excellent works related to studying nucleic acids with atomic force microscopy [1554-1575]. We believe that the remarkable interest in this application will continue growing in the future.

    ID Reference list (newly come references are marked red)
    37 Investigation of polystyrene nanoparticles and DNA-protein complexes by AFM with image reconstruction
    C.F. Zhu, I. Lee, X. Wang, C. Wang, C. Bai
    Applied Surface Science, 126 (1998), 3-4, 281-286
    113 AFM study of etching of cleaved 100 faces of L-arginine phosphate monohydrate single crystals. I. Dislocation etch pits and step bunching
    K. Sangwal, J. Servat, F. Sanz, J. Torrent-Burgues
    Journal of Crystal Growth, 180 (1997), 2, 263-273
    114 AFM study of etching of cleaved 100 faces of L-arginine phosphate monohydrate single crystals. II. Two-dimensional nucleation, formation of spiral elevations and decoration of dissolution layers
    K. Sangwal, J. Torrent-Burgues, F. Sanz, J. Servat
    Journal of Crystal Growth, 180 (1997), 2, 274-279
    256 STM and AFM of bio/organic molecules and structures
    A. Ikai
    Surface Science Reports, 26 (1997), 261-332
    321 Analysis of radiation damage of DNA by atomic force microscopy in comparison with agarose gel electrophoresis studies
    M. Murakami, H. Hirokawa, I. Hayata
    Journal of Biochemical and Biophysical Methods, 44 (2000), 1-2, 31-40
    352 Atomic force microscopy examination of tobacco mosaic virus and virion RNA
    Y.F. Drygin, M.O. Gallyamov, I.V. Yaminsky, O.A. Bordunova
    FEBS Letters, 425 (1998), 2, 217-221
    354 Atomic force microscopy for studying gene transfection mediated by cationic liposomes with a cationic cholesterol derivative
    T. Furuno, A. Noguchi, C. Kawaura, M. Nakanishi
    FEBS Letters, 421 (1998), 1, 69-72
    384 Atomic force microscopy of supercoiled DNA structure on mica
    T. Okada, M. Tanigawa
    Analytica Chimica Acta, 365 (1998), 1-3, 19-25
    523 High-resolution atomic-force microscopy of DNA: the pitch of the double helix
    J. Mou, D.M. Czajkowsky, Z. Yiyi, S. Zhifeng
    FEBS Letters, 371 (1995), 3 (September 11), 279-282
    560 Intercalation-induced changes in DNA supercoiling observed in real-time by atomic force microscopy
    C.A. Laughton, S.J.B. Tendler, P.M. Williams, C.J. Roberts, M.C. Davies, L.H. Pope
    Analytica Chimica Acta, 400 (1999), 1-3, 27-32
    652 Observation of single- and double-stranded DNA using non-contact atomic force microscopy
    T. Matsumoto, T. Kawai, Y. Maeda
    Applied Surface Science, 140 (1999), 3-4, 400-405
    657 Observations of cleavage steps, slip traces and dislocation hollow cores on cleaved 100 faces of L-arginine phosphate monohydrate single crystals by atomic force microscopy
    K. Sangwal, J. Torrent-Burgues, F. Sanz, J. Servat
    Surface Science, 374 (1997), 1-3, 387-396
    684 Recovery and amplification of plasmid DNA with atomic force microscopy and the polymerase chain reaction
    X.-M. Xu, A. Ikai
    Analytica Chimica Acta, 361 (1998), 1-2 (March 31), 1-7
    708 Structural analysis of heavy ion radiation-induced chromosome aberrations by atomic force microscopy
    M. Murakami, M. Minamihisamatsu, K. Sato, I. Hayata
    Journal of Biochemical and Biophysical Methods, 48 (2001), 3, 293-301
    790 Direct measurement of the forces between complementary strands of DNA
    G.U. Lee, L.A. Chrisey, R.J. Colton
    Science 266 (1994), 771
    876 MeV-atomic-ion-induced surface tracks in Langmuir-Blodgett films and l-valine crystals studied by scanning force microscopy
    C.T. Reimann, J. Kopniczky, E. Wistus, J. Eriksson, P. Hakansson, B.U.R. Sundqvist
    International Journal of Mass Spectrometry and Ion Processes, 151 (1995), 2-3, 147-158
    996 Stretching and breaking duplex DNA by chemical force microscopy
    Noy, A., Vezenov, D.V., Kayyem, J.F., Meade, T.J. and Lieber, C.M.
    Chem. Biol. 4 (1997), 519-527
    1000 A novel assay for drug-DNA binding mode, affinity, and exclusion number: Scanning force microscopy
    J.E. Coury, L. McFail-Isom, L.D. Williams, L.A. Bottomley
    Proc. Natl. Acad. Sci. USA 93 (1996) 12283-12286
    1024 Immobilization strategies for biological scanning probe microscopy
    P. Wagner
    FEBS Letters, 430 (1998), 1-2, 112-115
    1119 Visualization of supercoiled DNA with atomic force microscopy in situ
    Y.L. Lyubchenko, L.S. Shlyakhtenko
    Proc. Natl. Acad. Sci. USA 94 (1997) 496-501
    1124 Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure
    L.H. Pope, M.C. Davies, C.A. Laughton, C.J. Roberts, S.J.B. Tendler, P.M. Williams
    J. Microscopy 199 (2000) (1), 68-78
    1306 Structure and dynamics of supercoil-stabilized DNA cruciforms
    Shlyakhtenko L.S., Potaman V.N., Sinden R.R., Lyubchenko Y.L.
    J. Mol. Biol. 280 (1998), 61-72
    1506 STM and AFM images of nucleosome DNA under water
    S.M. Lindsay, L.A. Nagahara, T.Thundat, U. Knipping, R.L. Rill, B. Drake, C.B. Prater, A.L. Weisenhorn, S.A.C. Gould and P.K. Hansma
    J Biomol. Struct. Dynam. 7 (1989) 279
    1507 Imaging single-stranded DNA, antigen-antibody reaction and polymerized Langmuir-Blodgett films with an AFM
    A.L. Weisenhorn, H.E.Gaub, H.G.Hansma, R.L.Sinsheimer, G.L. Kelderman and P.K.Hansma
    Scanning Microsc. 4 (1990) 511
    1508 Molecular-resolution images of Langmuir-Blodgett films and DNA by atomic force microscopy
    A.L.Weisenhorn, M.Egger, F. Ohnesorge, S.A.C. Gould, S.-P. Heyn, L.Sinsheimer, H.E.Gaub, H.G.Hansma and P.K. Hansma
    Langmuir 7 (1991) 8
    1510 Circular DNA molecules imaged in air by scanning force microscopy
    C. Bustamante, J. Vesenka, C.L. Tang, W.Lees, M. Guthold and R. Keller
    Biochemistry 31 (1992) 22
    1511 Imaging and nanodissection of individual supercoiled plasmids by atomic force microscopy
    [published erratum appears in Nucleic Acids Res. 20(7)1992:1841]
    E. Henderson
    Nucleic Acids Res. 20 (1992) 445
    1529 Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces
    Lyubchenko Y.L., Oden P.I., Lampner D., Lindsay S.M., Dunker K.A.
    Nucl. Acids Res. (1993) 21: 1117??"1123
    1532 Atomic force microscopy of reovirus dsRNA: a routine technique for length measurements
    Y.L. Lyubchenko, B.L. Jacobs and S.M. Lindsay
    Nucleic Acids Res. 20 (1992) 3983
    1534 Atomic force microscopy of DNA molecules
    J.Yang, K.Takeyasu and Z.Shao
    FEBS Lett. 301 (1992) 173
    1536 Atomic Force Microscopy of Uncoated Plasmid DNA:Nanometer Resolution with only Nanogram Amounts of Sample
    M.Q.Li, H.G. Hansma, J. Vesenka, G. Kelderman and P.K.Hansma
    J.Biomol. Struct. Dynam. 10 (1992) 607
    1542 Humidity effects on atomic force microscopy of gold-labeled DNA on mica
    J.Vesenka, S. Manne, G.Yang, C.J. Bustamante and E.Henderson
    Scanning Microsc. 7 (1993) 781
    1543 Atomic Force Microscopy of DNA in Aqueous Solutions
    H.G.Hansma, M.Bezanilla, F.Zenhausen, M. Adrian and R. Sinsheimer
    Nucleic Acids Res. 21 (1993) 505
    1544 Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions
    M. Hegner, P. Wagner and G.Semenza
    FEBS Lett. 336 (1993) 452
    1545 Applications for Atomic Force Microscopy of DNA
    H.G. Hansma, D.E. Laney, M. Bezanilla, R.L. Sinsheimer and P.K. Hansma
    Biophys. J. 68 (1995) 1672
    1546 Following the Assembly of RNA Polymerase-DNA Complexes in Aqueous Solutions with the Scanning Force Microscope
    M. Guthold, M. Bezanilla, D.A. Erie, B. Jenkins, H.G. Hansma and C. Bustamante
    Proc. Natl. Acad. Sci. USA 91 (1994) 12927
    1547 Reproducible Imaging and Dissection of Plasmid DNA under Liquid with the Atomic Force Microscope
    H.G. Hansma, J. Vesenka, C. Siegerist, G. Kelderman, H. Morrett, R.L. Sinsheimer, V. Elings, C. Bustamante and P.K. Hansma
    Science 256 (1992) 1180
    1548 Atomic force microscopy of oriented linear DNA molecules labeled with 5 nm gold spheres
    W.L. Shaiu, D.D. Larson, J. Vesenka and E. Henderson
    Nucleic Acids Res. 21 (1993) 99
    1549 Observation of Binding and Polymerization of Fur Repressor onto Operator-Containing DNA with Electron and Atomic Force Microscopes
    E. Le Cam, D. Frechon, M. Barray, A. Fourgade and E. Delain
    Proc. Natl. Acad. Sci. USA 91 (1994) 11816
    1550 Bending and straightening of DNA induced by the same ligand: characterization with the atomic force microscope
    H.G. Hansma, K.A. Browne, M. Bezanilla and T.C. Bruice
    Biochemistry 33 (1994) 8436
    1551 Motion and enzymatic degradation of DNA in the atomic force microscope
    M. Bezanilla, B. Drake, E. Nudler, M. Kashlev, P.K. Hansma and H.G. Hansma
    Biophys. J. 67 (1994) 2454
    1552 Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies
    L.I. Pietrasanta, A. Schaper and T.M. Jopvin
    Nucleic Acids Res. 22 (1994) 3288
    1553 A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy
    T.C. Marsh, J.Vesenka and E. Henderson
    Nucleic Acids Res. 23 (1995) 696
    1554 Adsorption of DNA to mica, silylated mica and minerals: characterization by atomic force microscopy
    Bezanilla, M., S. Manne, D. E. Laney, Y. L. Lyubchenko, and H. G. Hansma
    Langmuir 11 (1995), 655-659
    1555 Atomic Force Microscopy of Biochemically Tagged DNA
    Murray, M. N., H. G. Hansma, M. Bezanilla, T. Sano, D. F. Ogletree, W. Kolbe, C. L. Smith, C. R. Cantor, S. Spengler, P. K. Hansma, and M. Salmeron
    Proc. Natl. Acad. Sci. USA 90 (1993), 3811-3814
    1556 Atomic force microscopy of biomolecules
    Hansma H. G.
    J. Vac. Sci. Technol. B14 (1996) 1390-1394
    1557 Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids
    Hansma H. G., I. Revenko K. Kim and D. E. Laney
    Nucleic Acids Res. 24 (1996), 713-720
    1558 Atomic force microscopy of single- and double-stranded DNA
    Hansma, H. G., R. L. Sinsheimer, M. Q. Li, and P. K. Hansma
    Nucleic Acids Res. 20 (1992), 3585-90
    1559 Bending and motion of DNA in the atomic force microscope. In Biological Structure and Dynamics
    Hansma H. G., D. E. Laney I. Revenko, K. Kim and J. P. Cleveland
    Adenine Press, Albany, NY. (1996) 249-258
    1560 Direct observation of one-dimensional diffusion and transcription by escherichia coli RNA polymerase
    Guthold, M., X. Zhu, C. Rivetti, G. Yang, N. H. Thomson, S. Kasas, H. G. Hansma, B. Smith, P. K. Hansma, and C. Bustamante
    Biophys. J. 77 (1999), 2284-94
    1561 DNA binding to mica correlates with cationic radius: assay by atomic force microscopy
    Hansma H. G. and D. E. Laney
    Biophys. J. 70 (1996), 1933-1939
    1562 DNA condensation for gene therapy as monitored by atomic force microscopy
    Hansma, H. G., R. Golan, W. Hsieh, C. P. Lollo, P. Mullen-Ley, and D. Kwoh
    Nucleic Acids Res. 26 (1998), 2481-2487
    1563 DNA toroids: stages in condensation
    Golan, R., L. I. Pietrasanta, W. Hsieh, and H. G. Hansma.
    Biochemistry. 38 (1999), 14069-14076
    1564 Escherichia coliRNA polymerase activity observed using atomic force microscopy
    Kasas, S., N. H. Thomson, B. L. Smith, H. G. Hansma, X. Zhu, M. Guthold, C. Bustamante, E. T. Kool, M. Kashlev, and P. K. Hansma
    Biochemistry, 36 (1997), 461-468
    1565 Left-handed orientation of histidine-tagged RNA polymerase complexes imaged by atomic force microscopy
    Hansma, H. G., M. Bezanilla, E. Nudler, P. K. Hansma, J. Hoh, M. Kashlev, N. Firouz, and B. Smith
    Probe Microscopy. 1 (1998), 117-125
    1566 Phase imaging of moving DNA molecules and DNA molecules replicated in the atomic force microscope
    Argaman, M., R. Golan, N. H. Thomson, and H. G. Hansma
    Nucleic Acids Res. 25 (1997), 4379-4384
    1567 Polymerase activities and RNA structures in the atomic force microscope
    Hansma, H. G., R. Golan, W. Hsieh, S. L. Daubendiek, and E. T. Kool
    J. Struct. Biol. 127 (1999) 240-247
    1568 Potential applications of atomic force microscopy of DNA to the human genome project
    Hansma, H. G., and P. K. Hansma
    Proc. SPIE - Int. Soc. Opt. Eng. (USA). 1891 (1993), 66-70
    1569 Probing biopolymers with the atomic force microscope: a review
    Hansma H.G., Pietrasanta L.I., Auerbach I.D., Sorenson C., Golan R., Holden P.A.
    Journal of Biomaterials Science. Polymer Edition 11 (2000), 7, 675-683
    1570 Probing the Sacchromyces cervisiae CBF3-CEN DNA kinetochore complex using atomic force microscopy
    Pietrasanta, L. I., D. Thrower, W. Hsieh, S. Rao, O. Stemmann, J. Lechner, J. Carbon, and H. G. Hansma
    Proc. Natl. Acad. Sci. USA 96 (1999), 3757-3762
    1571 Recent Advances in Atomic force Microscopy of DNA
    Hansma, H. G., R. L. Sinsheimer, J. Groppe, T. C. Bruice, V. Elings, G. Gurley, M. Bezanilla, I. A. Mastrangelo, P. V. C. Hough, and P. K. Hansma
    Scanning. 15 (1993), 296-299
    1572 Recent Highlights from Atomic Force Microscopy of DNA. Biological Structure and Dynamics
    Hansma H.G., Pietrasanta L.I., Golan R., Sitko J.C., Viani M., Paloczi G., Smith B.L., Thrower D., Hansma P.K.
    Conversation 11 (2000), 271-276
    1573 Structures of large T antigen at the origin of SV40 DNA replication by atomic force microscopy
    Mastrangelo, I. A., M. Bezanilla, P. K. Hansma, P. V. C. Hough, and H. G. Hansma
    Biophys. J. 66 (1994), 293-298
    1574 Surface Biology of DNA by Atomic Force Microscopy
    Hansma H.G.
    Ann. Rev. Physical Chemistry 52 (2001), 71-92
    1575 Varieties of imaging with scanning probe microscopes
    Hansma H. G.
    Proc. Natl. Acad. Sci. USA 96 (1999), 14678-14680
    1586 Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping Studied by Statistical Polymer Chain Analysis
    Rivetti, C., Guthold, M. and Bustamante, C.
    J. Mol. Biol. 264 (1996), 919-932
    1587 Properties of Biomolecules Measured from Atomic Force Microscope Images: A Review
    Hansma, H.G., Kim, K.J., Laney, D.E., Garcia, R.A., Argaman, M., Allen, M.J. and Parsons, S.M.
    J. Struct. Biol. 119(1997), 99-108
    1588 A high-resolution instrument that can operate in liquids is making complex biological structures accessible to study in conditions close to those that exist in living organisms
    C. Bustamante, D. Keller
    Phys. Today 48 (December) (1995), 33
    1589 Translating biomolecular recognition into nanomechanics
    Fritz J., Baller M.K., Lang H.P., Rothuizen H., Vettiger P., Meyer E., Guntherodt H.-J., Gerber Ch, Gimzewski J.K.
    Science, 288 (2000), 316-318
    1622 Stability of thiol-immobilized DNA on microcantilever sensors
    K.A. Stevenson, A. Mehta, K.M. Hansen and T.G. Thundat
    Proc. ESC 201 Meeting - Philadelphia, Pennsylvania, May 12-17 (2002)
    1213 Carbon-Nanotube Tip for Highly-Reproducible Imaging of Deoxyribonucleic Acid Helical Turns by Noncontact Atomic Force Microscopy
    T. Uchihashi, N. Choi, M. Tanigawa, M. Ashino, Y. Sugawara, H. Nishijima, S. Akita, Y. Nakayama, H. Tokumoto, K. Yokoyama, S. Morita and M. Ishikawa
    Jpn. J. Appl. Phys., 39 (2000) L887
    1215 Magnetic and acoustic tapping mode microscopy of liquid phase phospholipid bilayers and DNA molecules
    Irene Revenko and Roger Proksch
    J. Appl. Phys. 87 (2000) 526-533
    1251 Scanning Force Microscopy of Small Ligand-Nucleic Acid Complexes: Tris(o-phenanthroline)ruthenium(II)as a Test for a New Assay
    Joseph E. Coury, Jaimie R. Anderson, Lori McFail-Isom, Loren Dean Williams and Lawrence A. Bottomley
    J. Am. Chem. Soc. 119 (1997), 3792-3796
    1374 Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer
    A. Sanchez-Sevilla, J. Thimonier, M. Marilley, J. Rocca-Serra and J. Barbet
    Ultramicroscopy, 92 (2002) 3-4, pp. 151-158
    1390 DC electric-field-induced DNA stretching for AFM and SNOM studies
    J.M. Kim, T. Ohtani, J.Y. Park, S.M. Chang and H. Muramatsu
    Ultramicroscopy, 91 (2002) 1-4, pp. 139-149
    1443 Adsorption kinetics and mechanical properties of thiol-modified DNA-oligos on gold investigated by microcantilever sensors
    R. Marie, H. Jensenius, J. Thaysen, C. B. Christensen, A. Boisen
    Ultramicroscopy 91 (2002) 29-36
    1691 Strained DNA is kinked by low concentrations of Zn2+
    W. Han, M. Dlakic, Y. Zhu, S.M. Lindsay and R.E. Harrington
    Proc. Natl. Acad. Sci. USA 94 (1997), 10565-10570
    1694 Conformational transition in DNA on a cold surface
    Feng X.Z., Bash R., Balagurumoorthy P., Lohr D., Harrington R.E., Lindsay S.M.
    Nucleic Acids Res. 28 (2000), 593-596
    1695 The mechanical properties of single chromatin fibers under tension
    S.H. Leuba, J. Zlatanova, M.A. Karymov, R. Bash, Y.Z Liu, D. Lohr, R.E. Harrington and S.M. Lindsay
    Single Molecules 1 (2000), pp. 185-193
    1696 Mechanically stretching single chromatin fibers
    S.H. Leuba, M.A. Karymov, Y.Z. Liu, S.M. Lindsay and J. Zlatanova
    Gene Therapy and Molecular Biology 4 (2000), 297-301
    1697 Conformation and Rigidity of DNA Microcircles containing waf1 Response Element for P53 Regulatory Protein
    H. Zhou, Y. Zhang, Z.O. Yang, X.Z. Feng, S.M. Lindsay, P. Baalagurumoorthy and R.E. Harrington
    J. Mol. Biol. 306, 227-238 (2001)
    1702 Imaging Chromosome by a Lateral Force Microscope
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    Analytical Sciences, 16 (2000), 12, 1261-1264
    1704 Structural and topological differences between a glycopeptide-intermediate clinical strain and glycopeptide-susceptible strains of staphylococcus aureus revealed by atomic force microscopy
    Susan Boyle-Vavra, Jongin Hahm, S. J. Sibener, and Robert S. Daum
    Antimicrob. Agents Chemother., 44 (2000) pp. 3456 - 3460
    1705 The AFM as a tool for chromosomal dissection - the influence of physical parameters
    R.W. Stark, S. Thalhammer, J. Wienberg, W.M. Heckl
    Applied Physics A: Materials Science & Processing, 66 (1998) S579-S584
    1722 Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy
    Torunn Berge, Darren J. Ellis, David T. F. Dryden, J. Michael Edwardson, and Robert M. Henderson
    Biophys. J., 79 (2000) 479 - 484
    1739 Sequence-dependent DNA curvature and flexibility from scanning force microscopy images
    Anita Scipioni, Claudio Anselmi, Giampaolo Zuccheri, Bruno Samori, and Pasquale De Santis
    Biophys. J., 83 (2002) 2408 - 2418
    1748 Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy
    Mikio Kato, Chad J. McAllister, Shingo Hokabe, Nobuyoshi Shimizu, and Yuri L. Lyubchenko
    Eur. J. Biochem., 269 (2002) 3632 - 3636
    1757 Three-dimensional interaction of phi29 pRNA dimer probed by chemical modification interference, cryo-AFM, and cross-linking
    Yahya Mat-Arip, Kyle Garver, Chaoping Chen, Sitong Sheng, Zhifeng Shao, and Peixuan Guo
    J. Biol. Chem, 276 (2001) 32575 - 32584
    1758 Population analysis of subsaturated 172-12 nucleosomal arrays by atomic force microscopy detects nonrandom behavior that is favored by histone acetylation and short repeat length
    Ralph C. Bash, Jaya Yodh, Yuri Lyubchenko, Neal Woodbury, and D. Lohr
    J. Biol. Chem, 276 (2001) 48362 - 48370
    1765 Atomic force microscopy proposes a 'kiss and pull' mechanism for enhancer function
    Shige H. Yoshimura, Chikashi Yoshida, Kazuhiko Igarashi, and Kunio Takeyasu
    J. Electron Microsc. (Tokyo), 49 (2000) 407 - 413
    1774 Simultaneous collection of topographic and fluorescent images of barley chromosomes by scanning near-field optical/atomic force microscopy
    Tomoyuki Yoshino, Shigeru Sugiyama, Shoji Hagiwara, Tatsuo Ushiki, and Toshio Ohtani
    J. Electron Microsc. (Tokyo), 49 (2000) 199 - 203
    1781 The atomic force microscope as a new microdissecting tool for the generation of genetic probes
    Thalhammer, S., Stark, R. Muller, S., Wienberg, J. and Heckl, W.M.
    J. Struct. Biol. 119 (1997), 232-237
    1782 Chromosome classification by atomic force microscopy volume measurement
    T. J. McMaster, M. O. Winfield, A. A. Baker, A. Karp, M. J. Miles
    J. Vac. Sci. Technol. B14 (1996) 2, 1438-1443
    1784 GTG banding pattern on human metaphase chromosomes revealed by high resolution atomic-force microscopy
    S. Thalhammer, U. Koehler, R. W. Stark and W. M. Heckl
    Journal of Microscopy, 203, Pt 1, (2001) 1, pp. 1-5
    1788 Salt-Dependent Chromosome Viscoelasticity Characterized by Scanning Force Microscopy-Based Volume Measurements
    Wolfgang Fritzsche
    Microscopy Research and Technique 44 (1999) 357-362
    1789 Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips
    Gavin R. Schnitzler, Chin Li Cheung, Jason H. Hafner, Andrew J. Saurin, Robert E. Kingston, and Charles M. Lieber
    Mol. Cell. Biol., 21 (2001) 8504 - 8511
    1791 DNA monolayer on gold substrates characterized by nanoparticle labeling and scanning force microscopy
    A. Csaki, R. Moller, W. Straube, J. M. Kohler, and W. Fritzsche
    Nucleic Acids Res., 29 (2001) 81
    1792 Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
    Torunn Berge, Nigel S. Jenkins, Richard B. Hopkirk, Michael J. Waring, J. Michael Edwardson, and Robert M. Henderson
    Nucleic Acids Res., 30 (2002) 2980 - 2986
    1793 UV light-damaged DNA and its interaction with human replication protein A: an atomic force microscopy study
    M. Lysetska, A. Knoll, D. Boehringer, T. Hey, G. Krauss, and G. Krausch
    Nucleic Acids Res., 30 (2002) 2686 - 2691
    1794 Detection and mapping of mismatched base pairs in DNA molecules by atomic force microscopy
    Masato Tanigawa, Masanori Gotoh, Masayuki Machida, Takao Okada, and Michio Oishi
    Nucleic Acids Res., 28 (2000) 38
    1795 AFM characterization of single strand-specific endonuclease activity on linear DNA
    Kazuo Umemura, Fuji Nagami, Takao Okada, and Reiko Kuroda
    Nucleic Acids Res., 28 (2000) 39
    1796 DNA probes on chip surfaces studied by scanning force microscopy using specific binding of colloidal gold
    Robert Moller, Andrea Csaki, J. Michael Kohler, and Wolfgang Fritzsche
    Nucleic Acids Res., 28 (2000) 91
    1797 Structure and dynamics of three-way DNA junctions: atomic force microscopy studies
    Luda S. Shlyakhtenko, Vladimir N. Potaman, Richard R. Sinden, Alexander A. Gall, and Yuri L. Lyubchenko
    Nucleic Acids Res., 28 (2000) 3472 - 3477
    1798 H-NS mediated compaction of DNA visualised by atomic force microscopy
    Remus Thei Dame, Claire Wyman, and Nora Goosen
    Nucleic Acids Res., 28 (2000) 3504 - 3510
    1801 Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy
    Arnon Henn, Ohad Medalia, Shu-Ping Shi, Michal Steinberg, Francois Franceschi, and Irit Sagi
    PNAS, 98 (2001) 5007 - 5012
    1806 Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy
    Benoit Ladoux, Jean-Pierre Quivy, Patrick Doyle, Olivia du Roure, Genevieve Almouzni, and Jean-Louis Viovy
    PNAS, 97 (2000) 14251 - 14256
    1815 Numerical chromosomal abnormalities detected by atomic force microscopy
    Erg, N.M.A., Tan, E., Sahin, F.I. and Menevse, A.
    Scanning 21 (1999), 182-186
    2480 The chromatin structure of well-spread demembranated human sperm nuclei revealed by atomic force microscopy
    M. J. Allen, E. M. Bradbury, R. Balhorn
    Scanning Microsc., 10 (1996) 4, 989-994 (discussion 994-996)
    2557 Volume determination of human metaphase chromosomes by scanning force microscopy
    W. Fritzsche, E. Henderson
    Scanning Microsc., 10 (1996) 1, 103-110
    2487 The interaction of DNA with bacteriophage phi 29 connector: a study by AFM and TEM
    M. Valle, J. M. Valpuesta, J. L. Carrascosa, J. Tamayo, R. Garcia
    J. Struct. Biol., 116 (1996) 3, 390-398
    1939 Atomic force microscopy of DNA, nucleoproteins and cellular complexes: the use of functionalized substrates
    Y. L. Lyubchenko, R. E. Blankenship, A. A. Gall, S. M. Lindsay, O. Thiemann, L. Simpson, L. S. Shlyakhtenko
    Scanning Microsc. Suppl., 10 (1996) 97-109
    2186 Imaging of RNA in situ hybridization by atomic force microscopy
    W. H. Kalle, M. V. Macville, M. P. van de Corput, B. G. de Grooth, H. J. Tanke, A. K. Raap
    J. Microsc., 182 (1996) 3, 192-199
    2133 Extent of sperm chromatin hydration determined by atomic force microscopy
    M. J. Allen, J. D. th Lee, C. Lee, R. Balhorn
    Mol. Reprod. Dev., 45 (1996) 1, 87-92
    2286 Microscopic analysis of DNA and DNA-protein assembly by transmission electron microscopy, scanning tunneling microscopy and scanning force microscopy
    T. Muller-Reichert, H. Gross
    Scanning Microsc. Suppl., 10 (1996) 111-20 (discussion 120-121)
    2065 Deposition of supercoiled DNA on mica for scanning force microscopy imaging
    B. Samori, I. Muzzalupo, G. Zuccheri
    Scanning Microsc., 10 (1996) 4, 953-960 (discussion 960-962)
    2363 Quantitative analysis of the transcription factor AP2 binding to DNA by atomic force microscopy
    S. Nettikadan, F. Tokumasu, K. Takeyasu
    Biochemical and Biophysical Research Communications, 226 (1996) 3, 645-649
    1929 Atomic force microscopy investigation of radiation-induced DNA double strand breaks
    D. Pang, G. Popescu, J. Rodgers, B. L. Berman, A. Dritschilo
    Scanning Microsc., 10 (1996) 4, 1105-1110
    2265 Mapping individual cosmid DNAs by direct AFM imaging
    D. P. Allison, P. S. Kerper, M. J. Doktycz, T. Thundat, P. Modrich, F. W. Larimer, D. K. Johnson, P. R. Hoyt, M. L. Mucenski, R. J. Warmack
    Genomics, 41 (1997) 3, 379-384
    2264 Mapping elasticity of rehydrated metaphase chromosomes by scanning force microscopy
    W. Fritzsche, E. Henderson
    Ultramicroscopy, 69 (1997) 3, 191-200
    2454 Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution
    K. Rippe, N. Mucke, J. Langowski
    Nucleic Acids Res., 25 (1997) 9, 1736-1744
    2523 Transmission electron microscopy and scanning force microscopy of poly r(A-U) and poly r(A-U)-ethidium bromide
    J. Gilloteaux, J. M. Jamison, F. Zenhausern, M. Adrian, J. L. Summers
    Scanning, 19 (1997) 8, 523-532
    2242 Ku proteins join DNA fragments as shown by atomic force microscopy
    D. Pang, S. Yoo, W. S. Dynan, M. Jung, A. Dritschilo
    Cancer. Res., 57 (1997) 8, 1412-1415
    1975 Atomic force microscopy: a new way to look at chromatin
    M. J. Allen
    IEEE Eng Med Biol Mag, 16 (1997) 2, 34-41
    2025 Chicken erythrocyte nucleosomes have a defined orientation along the linker DNA--a scanning force microscopy study
    W. Fritzsche, E. Henderson
    Scanning, 19 (1997) 1, 42-47
    2522 Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coliRNA polymerase x sigma 54 holoenzyme by scanning force microscopy
    K. Rippe, M. Guthold, P. H. von Hippel, C. Bustamante
    J. Mol. Biol., 270 (1997) 2, 125-138
    2218 Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies
    M. Yaneva, T. Kowalewski, M. R. Lieber
    EMBO J., 16 (1997) 16, 5098-5112
    2545 Visualization and analysis of chromatin by scanning force microscopy
    C. Bustamante, G. Zuccheri, S. H. Leuba, G. Yang, B. Samori
    Methods, 12 (1997) 1, 73-83
    2550 Visualization of poly(A)-binding protein complex formation with poly(A) RNA using atomic force microscopy
    B. L. Smith, D. R. Gallie, H. Le, P. K. Hansma
    J. Struct. Biol., 119 (1997) 2, 109-117
    2551 Visualization of RNA crystal growth by atomic force microscopy
    J. D. Ng, Y. G. Kuznetsov, A. J. Malkin, G. Keith, R. Giege, A. McPherson
    Nucleic Acids Res., 25 (1997) 13, 2582-2588
    1906 Atomic force microscopy and cytochemistry of chromatin from marsupial spermatozoa with special reference to Sminthopsis crassicaudata
    L. L. Soon, C. Bottema, W. G. Breed
    Mol. Reprod. Dev., 48 (1997) 3, 367-374
    1898 Application of atomic force microscopy to visualization of DNA, chromatin, and chromosomes
    W. Fritzsche, L. Takac, E. Henderson
    Crit. Rev. Eukaryot. Gene. Expr., 7 (1997) 3, 231-240
    2547 Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM)
    R. L. Qian, Z. X. Liu, M. Y. Zhou, H. Y. Xie, C. Jiang, Z. J. Yan, M. Q. Li, Y. Zhang, J. Hu
    Cell. Res., 7 (1997) 2, 143-150
    2247 Linker histone tails and N-tails of histone H3 are redundant: scanning force microscopy studies of reconstituted fibers
    S. H. Leuba, C. Bustamante, K. van Holde, J. Zlatanova
    Biophys. J., 74 (1998) 6, 2830-2839
    2386 Scanning force microscopy of Escherichia coliRNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air
    A. Schulz, N. Mucke, J. Langowski, K. Rippe
    J. Mol. Biol., 283 (1998) 4, 821-836
    2370 Retrieval and amplification of single-copy genomic DNA from a nanometer region of chromosomes: a new and potential application of atomic force microscopy in genomic research
    X. M. Xu, A. Ikai
    Biochemical and Biophysical Research Communications, 248 (1998) 3, 744-748
    2027 Chromatin structure in bands and interbands of polytene chromosomes imaged by atomic force microscopy
    C. J. de Grauw, A. Avogadro, D. J. van den Heuvel, K. O. vd Werf, C. Otto, Y. Kraan, N. F. van Hulst, J. Greve
    J. Struct. Biol., 121 (1998) 1, 2-8
    2424 Solid-state DNA sizing by atomic force microscopy
    Y. Fang, T. S. Spisz, T. Wiltshire, N. P. D'Costa, I. N. Bankman, R. H. Reeves, J. H. Hoh
    Anal. Chem., 70 (1998) 10, 2123-2129
    1841 A convenient method of aligning large DNA molecules on bare mica surfaces for atomic force microscopy
    J. Li, C. Bai, C. Wang, C. Zhu, Z. Lin, Q. Li, E. Cao
    Nucleic Acids Res., 26 (1998) 20, 4785-4786
    2262 Mapping a protein-binding site on straightened DNA by atomic force microscopy
    H. Yokota, D. A. Nickerson, B. J. Trask, G. van den Engh, M. Hirst, I. Sadowski, R. Aebersold
    Anal. Biochem., 264 (1998) 2, 158-164
    2233 Investigation of neutron-induced damage in DNA by atomic force microscopy: experimental evidence of clustered DNA lesions
    D. Pang, B. L. Berman, S. Chasovskikh, J. E. Rodgers, A. Dritschilo
    Radiat Res, 150 (1998) 6, 612-618
    2447 Study of the interaction of DNA with cisplatin and other Pd(II) and Pt(II) complexes by atomic force microscopy
    G. B. Onoa, G. Cervantes, V. Moreno, M. J. Prieto
    Nucleic Acids Res., 26 (1998) 6, 1473-1480
    2052 Contributions of linker histones and histone H3 to chromatin structure: scanning force microscopy studies on trypsinized fibers
    S. H. Leuba, C. Bustamante, J. Zlatanova, K. van Holde
    Biophys. J., 74 (1998) 6, 2823-2829
    1852 A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays
    J. Reed, E. Singer, G. Kresbach, D. C. Schwartz
    Anal. Biochem., 259 (1998) 1, 80-88
    2495 The observation of the local ordering characteristics of spermidine-condensed DNA: atomic force microscopy and polarizing microscopy studies
    Z. Lin, C. Wang, X. Feng, M. Liu, J. Li, C. Bai
    Nucleic Acids Res., 26 (1998) 13, 3228-3234
    2240 Irreversible binding of poly(ADP)ribose polymerase cleavage product to DNA ends revealed by atomic force microscopy: possible role in apoptosis
    M. E. Smulson, D. Pang, M. Jung, A. Dimtchev, S. Chasovskikh, A. Spoonde, C. Simbulan-Rosenthal, D. Rosenthal, A. Yakovlev, A. Dritschilo
    Cancer. Res., 58 (1998) 16, 3495-3498
    2162 High resolution mapping DNAs by R-loop atomic force microscopy
    D. V. Klinov, I. V. Lagutina, V. V. Prokhorov, T. Neretina, P. P. Khil, Y. B. Lebedev, D. I. Cherny, V. V. Demin, E. D. Sverdlov
    Nucleic Acids Res., 26 (1998) 20, 4603-4610
    2553 Visualization of trp repressor and its complexes with DNA by atomic force microscopy
    E. Margeat, C. Le Grimellec, C. A. Royer
    Biophys. J., 75 (1998) 6, 2712-2720
    2385 Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet
    W. Wang, J. Lin, D. C. Schwartz
    Biophys. J., 75 (1998) 1, 513-520
    2087 Direct measurement of DNA by means of AFM
    M. Ueda, Y. Baba, H. Iwasaki, O. Kurosawa, M. Washizu
    Nucleic Acids Symp. Ser., 42 (1999) 245-246
    2203 In situ atomic force microscopy study of Alzheimer's beta-amyloid peptide on different substrates: new insights into mechanism of beta-sheet formation
    T. Kowalewski, D. M. Holtzman
    Proc. Natl. Acad. Sci. USA, 96 (1999) 7, 3688-3693
    2096 DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy
    J. van Noort, F. Orsini, A. Eker, C. Wyman, B. de Grooth, J. Greve
    Nucleic Acids Res., 27 (1999) 19, 3875-3880
    2404 Self-aggregation of DNA oligomers with XGG trinucleotide repeats: kinetic and atomic force microscopy measurements
    F. Sha, R. Mu, D. Henderson, F. M. Chen
    Biophys. J., 77 (1999) 1, 410-423
    2354 Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy
    L. I. Pietrasanta, D. Thrower, W. Hsieh, S. Rao, O. Stemmann, J. Lechner, J. Carbon, H. Hansma
    Proc. Natl. Acad. Sci. USA, 96 (1999) 7, 3757-3762
    2249 Lipid-induced organization of a primary amphipathic peptide: a coupled AFM-monolayer study
    N. Van Mau, V. Vie, L. Chaloin, E. Lesniewska, F. Heitz, C. Le Grimellec
    J. Membr. Biol., 167 (1999) 3, 241-249
    2196 Imaging the RecA-DNA complex by atomic force microscopy
    K. Umemura, S. Ikawa, T. Nishinaka, T. Shibata, R. Kuroda
    Nucleic Acids Symp. Ser., 42 (1999) 235-236
    1919 Atomic force microscopy imaging of DNA covalently immobilized on a functionalized mica substrate
    L. S. Shlyakhtenko, A. A. Gall, J. J. Weimer, D. D. Hawn, Y. L. Lyubchenko
    Biophys. J., 77 (1999) 1, 568-576
    2167 High-resolution AFM-imaging and mechanistic analysis of the 20 S proteasome
    I. T. Dorn, R. Eschrich, E. Seemuller, R. Guckenberger, R. Tampe
    J. Mol. Biol., 288 (1999) 5, 1027-1036
    2089 Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy
    D. J. Ellis, D. T. Dryden, T. Berge, J. M. Edwardson, R. M. Henderson
    Nat. Struct. Biol., 6 (1999) 1, 15-17
    1887 Analysis by atomic force microscopy of Med8 binding to cis-acting regulatory elements of the SUC2 and HXK2 genes of saccharomyces cerevisiae
    F. Moreno-Herrero, P. Herrero, J. Colchero, A. M. Baro, F. Moreno
    FEBS Letters, 459 (1999) 3, 427-432
    2439 Structure of branched DNA molecules: gel retardation and atomic force microscopy studies
    E. A. Oussatcheva, L. S. Shlyakhtenko, R. Glass, R. R. Sinden, Y. L. Lyubchenko, V. N. Potaman
    J. Mol. Biol., 292 (1999) 1, 75-86
    2429 Spin-stretching of DNA and protein molecules for detection by fluorescence and atomic force microscopy
    H. Yokota, J. Sunwoo, M. Sarikaya, G. van den Engh, R. Aebersold
    Anal. Chem., 71 (1999) 19, 4418-4422
    2501 The structure of the nucleosome core particle of chromatin in chicken erythrocytes visualized by using atomic force microscopy
    H. Zhao, Y. Zhang, S. B. Zhang, C. Jiang, Q. Y. He, M. Q. Li, R. L. Qian
    Cell. Res., 9 (1999) 4, 255-260
    1876 AFM study of membrane proteins, cytochrome P450 2B4, and NADPH-cytochrome P450 reductase and their complex formation
    O. I. Kiselyova, I. V. Yaminsky, Y. D. Ivanov, I. P. Kanaeva, V. Y. Kuznetsov, A. I. Archakov
    Arch. Biochem. Biophys., 371 (1999) 1, 1-7
    1959 Atomic force microscopy sees nucleosome positioning and histone H1-induced compaction in reconstituted chromatin
    M. H. Sato, K. Ura, K. I. Hohmura, F. Tokumasu, S. H. Yoshimura, F. Hanaoka, K. Takeyasu
    FEBS Letters, 452 (1999) 3, 267-271
    1889 Analysis of chromatin by scanning force microscopy
    S. H. Leuba, C. Bustamante
    Methods Mol. Biol., 119 (1999) 143-160
    2403 Selective cleaning of the cell debris in human chromosome preparations studied by scanning force microscopy
    J. Tamayo, M. Miles, A. Thein, P. Soothill
    J. Struct. Biol., 128 (1999) 2, 200-210
    2094 Discrimination of DNA hybridization using chemical force microscopy
    L. T. Mazzola, C. W. Frank, S. P. Fodor, C. Mosher, R. Lartius, E. Henderson
    Biophys. J., 76 (1999) 6, 2922-2933
    2157 Haplotyping by atomic force microscopy
    M. Sinclair
    Nature Biotechnology, 18 (2000) 7, 703
    1902 Atomic force and electron microscopy of high molecular weight circular DNA complexes with synthetic oligopeptide trivaline
    L. P. Martinkina, D. V. Klinov, A. A. Kolesnikov, V. Y. Yurchenko, S. A. Streltsov, T. V. Neretina, V. V. Demin, Y. Y. Vengerov
    J. Biomol. Struct. Dyn., 17 (2000) 4, 687-695
    1904 Atomic force microscopy analysis of intermediates in cobalt hexammine-induced DNA condensation
    D. Liu, C. Wang, J. Li, Z. Lin, Z. Tan, C. Bai
    J. Biomol. Struct. Dyn., 18 (2000) 1, 1-9
    1916 Atomic force microscopy examination of conformations of polynucleotides in response to platinum isomers: significance of GC content at broken ends
    D. Pang, S. Chasovskikh, J. S. Cohen, C. Obcemea, A. Dritschilo
    Int. J. Cancer, 90 (2000) 2, 68-72
    1938 Atomic force microscopy of DNA molecules stretched by spin-coating technique
    J. Y. Ye, K. Umemura, M. Ishikawa, R. Kuroda
    Anal. Biochem., 281 (2000) 1, 21-25
    1949 Atomic force microscopy of parallel DNA branched junction arrays
    R. Sha, F. Liu, D. P. Millar, N. C. Seeman
    Chem. Biol., 7 (2000) 9, 743-751
    2206 In Situ Observation of Growth Process of alpha-L-Glutamic Acid with Atomic Force Microscopy
    M. Kitamura, K. Onuma
    J. Colloid. Interface. Sci., 224 (2000) 2, 311-316
    2045 Complementary visualization of mitotic barley chromatin by field-emission scanning electron microscopy and scanning force microscopy
    A. Schaper, M. Rossle, H. Formanek, T. M. Jovin, G. Wanner
    J. Struct. Biol., 129 (2000) 1, 17-29
    2388 Scanning force microscopy of the complexes of p53 core domain with supercoiled DNA
    S. D. Jett, D. I. Cherny, V. Subramaniam, T. M. Jovin
    J. Mol. Biol., 299 (2000) 3, 585-592
    2170 Human chromosome structure studied by scanning force microscopy after an enzymatic digestion of the covering cell material
    J. Tamayo, M. Miles
    Ultramicroscopy, 82 (2000) 1-4, 245-251
    2072 Determination of preferential binding sites for anti-dsRNA antibodies on double-stranded RNA by scanning force microscopy
    M. Bonin, J. Oberstrass, N. Lukacs, K. Ewert, E. Oesterschulze, R. Kassing, W. Nellen
    RNA, 6 (2000) 4, 563-570
    2333 P67-phox-mediated NADPH oxidase assembly: imaging of cytochrome b558 liposomes by atomic force microscopy
    M. H. Paclet, A. W. Coleman, S. Vergnaud, F. Morel
    Biochemistry, 39 (2000) 31, 9302-9310
    2420 Single-molecular AFM probing of specific DNA sequencing using RecA-promoted homologous pairing and strand exchange
    G. H. Seong, T. Niimi, Y. Yanagida, E. Kobatake, M. Aizawa
    Anal. Chem., 72 (2000) 6, 1288-1293
    2441 Structures of Fibrous Supramolecular Assemblies Constructed by Amino Acid Surfactants: Investigation by AFM, SANS, and SAXS
    T. Imae, N. Hayashi, T. Matsumoto, T. Tada, M. Furusaka
    J. Colloid. Interface. Sci., 225 (2000) 2, 285-290
    2438 Structure of a fusion peptide analogue at the air-water interface, determined from surface activity, infrared spectroscopy and scanning force microscopy
    S. E. Taylor, B. Desbat, D. Blaudez, S. Jacobi, L. F. Chi, H. Fuchs, G. Schwarz
    Biophys. Chem., 87 (2000) 1, 63-72
    2492 The mechanism of G-banding detected by atomic force microscopy
    F. I. Sahin, M. A. Ergun, E. Tan, A. Menevse
    Scanning, 22 (2000) 1, 24-27
    2304 MutS-mediated detection of DNA mismatches using atomic force microscopy
    H. B. Sun, H. Yokota
    Anal. Chem., 72 (2000) 14, 3138-3141
    1957 Atomic force microscopy proposes a 'kiss and pull' mechanism for enhancer function
    S. H. Yoshimura, C. Yoshida, K. Igarashi, K. Takeyasu
    J. Electron Microsc. (Tokyo), 49 (2000) 3, 407-413
    2279 Method for orienting DNA molecules on mica surfaces in one direction for atomic force microscopy imaging
    M. Gad, M. Machida, W. Mizutani, M. Ishikawa
    J. Biomol. Struct. Dyn., 19 (2001) 3, 471-477
    2086 Direct measurement of conformational changes on DNA molecule intercalating with a fluorescence dye in an electrophoretic buffer solution by means of atomic force microscopy
    N. Kaji, M. Ueda, Y. Baba
    Electrophoresis, 22 (2001) 16, 3357-3364
    2061 Cu(2+) Inhibits the Aggregation of Amyloid beta-Peptide(1-42) in vitro
    J. Zou, K. Kajita, N. Sugimoto
    Angew. Chem. Int. Ed. Engl., 40 (2001) 12, 2274-2277
    2054 Controlled immobilization of DNA molecules using chemical modification of mica surfaces for atomic force microscopy: characterization in air
    K. Umemura, M. Ishikawa, R. Kuroda
    Anal. Biochem., 290 (2001) 2, 232-237
    2068 Detection of abasic sites on individual DNA molecules using atomic force microscopy
    H. B. Sun, L. Qian, H. Yokota
    Anal. Chem., 73 (2001) 10, 2229-2232
    2028 Chromosome elasticity and mitotic polar ejection force measured in living Drosophila embryos by four-dimensional microscopy-based motion analysis
    W. F. Marshall, J. F. Marko, D. A. Agard, J. W. Sedat
    Curr. Biol., 11 (2001) 8, 569-578
    1920 Atomic force microscopy imaging of DNA-cationic liposome complexes optimised for gene transfection into neuronal cells
    L. A. Wangerek, H. H. Dahl, T. J. Senden, J. B. Carlin, D. A. Jans, D. E. Dunstan, P. A. Ioannou, R. Williamson, S. M. Forrest
    J. Gene. Med., 3 (2001) 1, 72-81
    1937 Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates
    Y. L. Lyubchenko, A. A. Gall, L. S. Shlyakhtenko
    Methods Mol. Biol., 148 (2001) 569-578
    2048 Confocal and probe microscopy to study gene transfection mediated by cationic liposomes with a cationic cholesterol derivative
    M. Nakanishi, A. Noguchi
    Adv. Drug. Deliv. Rev., 52 (2001) 3, 197-207
    1999 C-banding visualized by atomic force microscopy
    E. Tan, F. I. Sahin, M. A. Ergun, I. Ercan, A. Menevse
    Scanning, 23 (2001) 1, 32-35
    2019 Charge-dependent sidedness of cytochrome P450 forms studied by quartz crystal microbalance and atomic force microscopy
    J. B. Schenkman, I. Jansson, Y. Lvov, J. F. Rusling, S. Boussaad, N. J. Tao
    Arch. Biochem. Biophys., 385 (2001) 1, 78-87
    1985 Binding of IRE-BP to its cognate RNA sequence: SFM studies on a universal RNA backbone for the analysis of RNA-protein interaction
    M. Bonin, J. Oberstrass, U. Vogt, M. Wassenegger, W. Nellen
    Biol. Chem., 382 (2001) 8, 1157-1162
    2394 Scanning force microscopy study on a single-stranded DNA: the genome of parvovirus B19
    G. Zuccheri, A. Bergia, G. Gallinella, M. Musiani, B. Samori
    Chembiochem., 2 (2001) 3, 199-204
    2342 Plasmid DNA network on a mica substrate investigated by atomic force microscopy
    A. Wu, Z. Li, L. Yu, H. Wang, E. Wang
    Anal. Sci., 17 (2001) 5, 583-584
    2500 The structure of intramolecular triplex DNA: atomic force microscopy study
    W. J. Tiner, Sr., V. N. Potaman, R. R. Sinden, Y. L. Lyubchenko
    J. Mol. Biol., 314 (2001) 3, 353-357
    1872 AFM imaging in solution of protein-DNA complexes formed on DNA anchored to a gold surface
    O. Medalia, J. Englander, R. Guckenberger, J. Sperling
    Ultramicroscopy, 90 (2001) 2-3, 103-112
    1863 Adhesion Forces between LewisX Determinant Antigens as Measured by Atomic Force Microscopy
    C. Tromas, J. Rojo, J. M. De La Fuente, A. G. Barrientos, R. Garcia, S. Penades
    Angew. Chem. Int. Ed. Engl., 40 (2001) 16, 3052-3055
    1860 Accurate length determination of DNA molecules visualized by atomic force microscopy: evidence for a partial B- to A-form transition on mica
    C. Rivetti, S. Codeluppi
    Ultramicroscopy, 87 (2001) 1-2, 55-66
    1822 Atomic Force Microscopy of Rec.A-DNA Complexes Using a Carbon nanotube Tip
    K. Umemura, J. Komatsu, T. Uchihashi, N. Choi, S. Ikawa, T. Nishinaka, T. Shibata, Y. Nakayama, S. Katsura, A. Mizuno, H. Tokumoto, M. Ishikawa, and R. Kuroda
    Biochemical and Biophysical Research Communications, 281 (2001) 2, 390-395
    2541 Viewing of complex molecules of ethidium bromide and plasmid DNA in solution by atomic force microscopy
    K. Utsuno, M. Tsuboi, S. Katsumata, T. Iwamoto
    Chem. Pharm. Bull. (Tokyo), 49 (2001) 4, 413-417
    2540 Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ions: VCD and AFM evidence of DNA condensation
    V. Andrushchenko, Z. Leonenko, D. Cramb, H. van de Sande, H. Wieser
    Biopolymers, 61 (2001) 4, 243-260
    2510 Three-dimensional structure of G-banded human metaphase chromosomes observed by atomic force microscopy
    O. Hoshi, T. Ushiki
    Arch. Histol. Cytol., 64 (2001) 5, 475-482
    2427 Spin-column isolation of DNA-protein interactions from complex protein mixtures for AFM imaging
    P. R. Hoyt, M. J. Doktycz, R. J. Warmack, D. P. Allison
    Ultramicroscopy, 86 (2001) 1-2, 139-143
    2387 Scanning force microscopy of nucleic acid complexes
    P. T. Lillehei, L. A. Bottomley
    Methods Enzymol., 340 (2001) 234-251
    2097 DNA properties investigated by dynamic force microscopy
    L. Nony, R. Boisgard, J. P. Aime
    Biomacromolecules, 2 (2001) 3, 827-835
    2301 Monitoring DNA immobilization and hybridization on surfaces by atomic force microscopy force measurements
    J. Wang, A. J. Bard
    Anal. Chem., 73 (2001) 10, 2207-2212
    2101 Dynamic interactions of p53 with DNA in solution by time-lapse atomic force microscopy
    Y. Jiao, D. I. Cherny, G. Heim, T. M. Jovin, T. E. Schaffer
    J. Mol. Biol., 314 (2001) 2, 233-243
    2177 Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy
    F. Moreno-Herrero, P. Herrero, J. Colchero, A. M. Baro, F. Moreno
    Biochemical and Biophysical Research Communications, 280 (2001) 1, 151-157
    2107 Effect of poly(ADP-ribosyl)ation and Mg2+ ions on chromatin structure revealed by scanning force microscopy
    M. d'Erme, G. Yang, E. Sheagly, F. Palitti, C. Bustamante
    Biochemistry, 40 (2001) 37, 10947-10955
    2116 Electron and scanning force microscopy studies of alterations in supercoiled DNA tertiary structure
    D. I. Cherny, T. M. Jovin
    J. Mol. Biol., 313 (2001) 2, 295-307
    2270 Measurement of the length of the a helical section of a peptide directly using atomic force microscopy
    S. Takeda, R. Ptak, C. Nakamura, J. Miyake, M. Kageshima, S. P. Jarvis, H. Tokumoto
    Chem. Pharm. Bull. (Tokyo), 49 (2001) 12, 1512-1516
    2187 Imaging of single hairpin ribozymes in solution by atomic force microscopy
    M. J. Fay, N. G. Walter, J. M. Burke
    RNA, 7 (2001) 6, 887-895
    2201 Improvement of DNA-visualization in dynamic mode atomic force microscopy in air
    F. Noll, B. Geisler, N. Hampp
    Scanning, 23 (2001) 3, 175-181
    2235 Investigation of radiation damage in DNA by using atomic force microscopy
    S. Boichot, M. Fromm, S. Cunniffe, P. O'Neill, J. C. Labrune, A. Chambaudet, E. Delain, E. Le Cam
    Radiat Prot Dosimetry, 99 (2002) 1-4, 143-145
    2548 Visualization of complexes of Hoechst 33258 and DNA duplexes in solution by atomic force microscopy
    K. Utsuno, M. Tsuboi, S. Katsumata, T. Iwamoto
    Chem. Pharm. Bull. (Tokyo), 50 (2002) 2, 216-219
    2392 Scanning force microscopy studies on the structure and dynamics of single DNA molecules
    G. Zuccheri, B. Samori
    Methods Cell Biol., 68 (2002) 357-395
    1967 Atomic force microscopy study of the effects of Mg(2+) and other divalent cations on the end-to-end DNA interactions
    P. R. Dahlgren, Y. L. Lyubchenko
    Biochemistry, 41 (2002) 38, 11372-11378
    2071 Determination of a translocation chromosome by atomic force microscopy
    M. A. Ergun, M. Y. Karaoguz, G. D. Ince, E. Tan, A. Menevse
    Scanning, 24 (2002) 4, 204-206
    2453 Substrate-facilitated assembly of elastin-like peptides: studies by variable-temperature in situ atomic force microscopy
    G. Yang, K. A. Woodhouse, C. M. Yip
    J. Am. Chem. Soc., 124 (2002) 36, 10648-10649
    2448 Study of the modifications caused by cisplatin, transplatin, and Pd(II) and Pt(II) mepirizole derivatives on pBR322 DNA by atomic force microscopy
    G. B. Onoa, V. Moreno
    Int. J. Pharm., 245 (2002) 1-2, 55-65
    2267 Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation
    J. G. Yodh, N. Woodbury, L. S. Shlyakhtenko, Y. L. Lyubchenko, D. Lohr
    Biochemistry, 41 (2002) 11, 3565-3574
    2084 Direct atomic force microscopy visualization of integration host factor-induced DNA bending structure of the promoter regulatory region on the Pseudomonas TOL plasmid
    G. H. Seong, E. Kobatake, K. Miura, A. Nakazawa, M. Aizawa
    Biochemical and Biophysical Research Communications, 291 (2002) 2, 361-366
    1918 Atomic force microscopy identification of transcription factor NFkappaB bound to streptavidin-pin-holding DNA probe
    G. H. Seong, Y. Yanagida, M. Aizawa, E. Kobatake
    Anal. Biochem., 309 (2002) 2, 241-247
    2329 Optical biosensor and scanning probe microscopy studies of cytochrome P450 interactions with redox partners and phospholipid layers
    A. I. Archakov, Y. D. Ivanov
    Methods Enzymol., 357 (2002) 94-103
    2512 Time-lapse imaging of conformational changes in supercoiled DNA by scanning force microscopy
    F. Nagami, G. Zuccheri, B. Samori, R. Kuroda
    Anal. Biochem., 300 (2002) 2, 170-176
    2564 Comparison Between Shear Force and Tapping Mode AFM - High Resolution Imaging of DNA
    Massimo Antognozzi, Mark D. Szczelkun, Andrew N. Round and Mervyn J. Miles
    Single Mol., 3 (2002) 2-3, 105-110
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