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 |
| 1507 1508 |
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. |
| 1552 1553 |
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 |