SPM Applications in Studying 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 AFM 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±0.4nm 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 AFM 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 AFM 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 an AFM 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 AFM 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]. 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
H. Wang, Y. Sun, Zh. Li, E. Wang, B. Huang
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