Supercoiled plasmids deposited on freshly cleaved mica are normally loosely coiled, unless uranyl-acetate is used in the dehydration phase to pre-serve the structure of the molecules Ch
Trang 1itself approximately 18 times on average When not complexed with proteins (like in nucleosomes), the supercoiled DNA should be in the interwound form, which is called
“plectonemic.”
What is almost constantly found in the SFM literature is the imaging of DNA plasmids that simply do not appear plectonemic, even if the authors describe them as supercoiled Among other researchers, we have seen and reported plasmids that appeared too loosely coiled for their native superhelical density A comparison between theoretical and com-putational evaluations would also suggest that plasmids with a native superhelical density should be significantly more coiled under the conditions of SFM imaging (Vologodskii, 1992; Vologodskii and Cozzarelli, 1994) The shape of supercoiled plasmids in SFM images is often very open, with only one or two apparent crossovers Sometimes it is dif-ficult to distinguish the loosely coiled plasmids from the relaxed plasmids that can have
“random flops,” especially if they are very long At times, strange looking supercoiled plasmids have been presented The superhelical density should be spread homogeneously along the entire length of the molecule, where no extended sections have a significantly looser appearance On the contrary, many reports show plasmids with apparently highly
coiled sections and other sections which are completely loose (Pope et al., 2000) It is our
understanding that this could be due to local condensation conditions, which can drive some strand-to-strand contacts not only due to supercoiling Under the conditions of DNA deposition and dehydration adopted for SFM imaging, some condensation could occur, especially if enabled by the superhelical tension These conditions could even drive the molecules toward unnatural shapes A seriously limited number of EM studies demonstrate nicely interwound plectonemic plasmids; among them, the cryo-EM studies
demonstrate the nicest ones (Adrian et al., 1990) As mentioned earlier, the cryo-EM pic-tures generated much criticism (Gebe et al., 1996) Theoretical evaluations suggest that
the motivation of the highly coiled forms is due to the very low temperature equilibration
of the plasmids (Gebe et al., 1996) Evidence is building toward the idea that under the
normal conditions of imaging the observed shapes are normally fairly loose If the ionic strength of the solution to deposit is very high, then the deposited plasmids can appear
as highly coiled A good example is that of Lyubchenko and Shlyakhtenko (1997), who produced very nice images by depositing on AP-mica a plasmid solution with a very high concentration of NaCl Supercoiled plasmids deposited on freshly cleaved mica are normally loosely coiled, unless uranyl-acetate is used in the dehydration phase to
pre-serve the structure of the molecules (Cherny et al., 1998; F Nagami et al., unpublished
results) In this case (see Fig 8), the plasmids can be highly coiled, and it is very easy
to distinguish between relaxed and supercoiled plasmids in which case, the statistical evaluation of the two populations is very similar to the quantitative analysis by agarose gel electrophoresis On the other hand, in a few cases, very coiled plasmids were imaged
at low ionic strength on either freshly cleaved mica or oxidized silicon (Hansma et al., 1996; Yoshimura et al., 2000).
Under high ionic strength conditions, plasmids are extremely coiled and can be seen
as coiled on the surfaces especially if the experimental conditions (AP-mica or uranyl acetate) can limit their mobility before the ionic conditions are changed (e.g., in a rinsing step) Uranyl acetate might have the dual role of limiting the mobility and increasing the ionic strength (Not all salts would work in this way.)
Trang 2Fig 8 SFM image of plasmid DNA deposited on freshly cleaved mica and dehydrated from a solution containing uranyl acetate Highly supercoiled, completely relaxed, and fragmented linear DNA molecules are very easy to distinguish from the images under these conditions Courtesy of Fuji Nagami (F Nagami,
G Zuccheri, B Samor`ı, and R Kuroda (2002) Time-lapse imaging of conformational changes in supercoiled
DNA by scanning force microscopy Anal Biochem 300, 170 –176).
Thus, why are the same plasmids so loosely coiled under conditions that should still preserve their coiling? We presently believe that the electrostatic interactions with the surface and the statistical effects of being confined in a very thin layer of solution strongly increase the intramolecular strand-to-strand repulsion The electrostatic repulsion should keep the DNA strands apart, and thus uncoil them, except in the presence of a high con-centration of salt that screens the charges The natural partition of a linking deficit in DNA between writhing and twisting of the chain might be altered in favor of twisting under these conditions We are not aware of computer simulations that consider these factors
to determine the partition of supercoiling under strongly spatially confined conditions.
A partial B-to-A transition has been known to occur on DNA on the surface of mica (see Section III,E) Under these conditions, the superhelical tension should be greatly
reduced (Krylov et al., 1990) and might help to bring the supercoiled DNA to a low
state of coiling It appears to us that the shape of supercoiled DNA evidenced from SFM images could be the result of multiple factors and further evidences are awaited to completely clarify the issue.
Imaging supercoiled DNA in fluid at high ionic strength seems to be the only safe method to have nice plectonemic DNA on freshly cleaved mica under completely con-trolled conditions and without the aid of extraneous molecules To image plectonemic DNA in air, strongly adhesive surfaces (like AP-mica) need to be coupled to the high-ionic-strength environment Nicked plasmids appear open on freshly cleaved mica since they have the mobility to respond to the high electrostatic repulsion between strands This same repulsion that opens them up like circles is also responsible for the self-avoiding that causes DNA strands to never overlap if imaged on mica under nontrapping
Trang 3conditions (Rivetti et al., 1996) When imaged under trapping conditions, supercoiled
DNA might appear more nicely plectonemic Unfortunately, under the same conditions, nicked plasmids might display many chain crossovers, due to their random adsorption and trapping on the surface (such as for the many rosette-like shapes shown by Lyubchenko and Shlyakhlenko, 1997), and they will be more difficult to visualize and characterize.
VIII Conclusions and Perspectives
After several years of SFM experiments on DNA, there are many questions that micro-scopists would still like to answer Newer techniques and instruments are still emerging, often from the close collaboration of chemists and biologists with physicists Newer technologies and interdisciplinary approaches will certainly expand the knowledge on the structure and behavior of DNA in the following years.
A SFM Single-Molecule Stretching Experiments on DNA: Only a Brief Note
on a Booming Issue
The last few years have seen the emergence of force spectroscopy as a new field of research Using several kinds of force transducers, measured small forces can be applied
to properly selected parts of a molecule in order to study its behavior and the forces that hold its structure together The SFM cantilever is one of the most frequently used force transducers for force spectroscopy Many groups are already working in SFM force spectroscopy of DNA, studying the forces that not only keep the double helix together but also might determine its behavior in the interaction with proteins or other molecules
(Clausen-Schaumann et al., 2000; Lee et al., 1994; Noy et al., 1997; Strunz et al., 2000; Strunz et al., 1999).
B The Structure of ss-DNA
Relatively few SFM studies have been done on single-stranded nucleic acids Some possible reasons are the variability, complexity, and fragility of their structures Recent studies have shown that some useful information can also be gathered from
single-stranded DNA (Zuccheri et al., 2000) It can be easily predicted that some of the numerous
interesting questions regarding single-stranded DNA and RNA will find answers as a result of SFM studies.
Acknowledgments
We are grateful to Pasquale De Santis (University La Sapienza, Rome, Italy) for the very helpful discussion
on DNA curvature and flexibility, to Giuseppe Gargiulo (University of Bologna, Italy) for sharing his DNA constructs, and to Fuji Nagami (University of Tokyo, Japan) not only for helpful discussion but also for sharing his images of supercoiled plasmids This work was supported by Programmi Biotecnologie Legge 95/95 (MURST 5%); MURST PRIN (Progetti Biologia Strutturale 1997–1999 and 1999–2001)
Trang 4Adrian, M., Ten Heggeler-Bordier, B., Wahli, W., Stasiak, A Z., Stasiak, A., and Dubochet, J (1990) Direct
visualization of supercoiled DNA molecules in solution EMBO J 9(13), 4551–4554.
Aich, P., Labiuk, S L., Tari, L W., Delbaere, L J., Roesler, W J., Falk, K J., Steer, R P., and Lee, J S (1999)
M-DNA: A complex between divalent metal ions and DNA which behaves as a molecular wire J Mol Biol.
294(2), 477–485.
Anselmi, C., Bocchinfuso, G., De Santis, P., Savino, M., and Scipioni, A (1999) Dual role of DNA intrinsic
curvature and flexibility in determining nucleosome stability J Mol Biol 286(5), 1293–1301.
Argaman, M., Golan, R., Thomson, N H., and Hansma, H G (1997) Phase imaging of moving DNA molecules
and DNA molecules replicated in the atomic force microscope Nucl Acids Res 25(21), 4379–4384.
Bamdad, C (1998) A DNA self-assembled monolayer for the specific attachment of unmodified double- or
single-stranded DNA Biophys J 75(4), 1997–2003.
Bates, A D., and Maxwell, A (1993) “DNA Topology.” Oxford, New York; IRL Press, Oxford University Press
Baur, C., Gazen, B C., Koel, B., Ramachandran, T R., Requicha, A A G., and Zini, L (1997) Robotic
nanomanipulation with a scanning probe microscope in a networked computing environment J Vacuum
Sci Technol B (Microelectronics and Nanometer Structures) 15(4), 1577–1580.
Bednar, J., Furrer, P., Katritch, V., Stasiak, A Z., Dubochet, J., and Stasiak, A (1995) Determination of DNA persistence length by cryo-electron microscopy Separation of the static and dynamic contributions to the
apparent persistence length of DNA J Mol Biol 254(4), 579–594.
Bettini, A., Pozzan, M., Valdevit, E., and Frontali, C (1980) Microscopic persistence length of native DNA:
its relation to average molecular dimensions Biopolymers 19, 1689–1694.
Bezanilla, M., Brake, B., Nudler, E., Kashlev, M., Hansma, P K., and Hansma, H G (1994) Motion and
enzymatic degradation of DNA in the atomic force microscope Biophys J 67(6), 2454–2459.
Bezanilla, M., Manne, S., Laney, D E., Lyubchenko, Y L., and Hansma, H G (1995) Adsorption of DNA to
mica, silylated mica, and minerals—Characterization by atomic force microscopy Langmuir 11(2), 655–
659
Binnig, G (1992) Force microscopy Ultramicroscopy 42(JUL), 7–15.
Binnig, G., Quate, C F., and Gerber, C (1986) Atomic force microscope Phys Rev Lett 56(9), 930–
933
Binnig, G., and Rohrer, H (1984) Scanning tunnelling microscopy In “Trends in Physics” (J Janta and
J Pantoflicek, eds.) Vol 1, 38– 48 European Physical Society, Prague
Binnig, G., Rohrer, H., Gerber, C., and Weibel, E (1982a) Surface studies by scanning tunneling microscopy
Phys Rev Lett 49, 57–61.
Binnig, G., Rohrer, H., Gerber, C., and Weibel, E (1982b) Tunneling through a controllable vacuum gap
Appl Phys Lett 40(2), 178–180.
Boles, T C., White, J H., and Cozzarelli, N R (1990) Structure of plectonemically supercoiled DNA J Mol.
Biol 213(4) 931–951.
Bustamante, C., Guthold, M., Zhu, X., and Yang, G (1999) Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in
liquid J Biol Chem 274(24), 16,665–16,668.
Bustamante, C., and Rivetti, C (1996) Visualizing protein-nucleic acid interactions on a large scale with the
scanning force microscope Annu Rev Biophys Biomol Struct 25, 395– 429.
Bustamante, C., Vesenka, J., Tang, C L., Rees, W., Guthold, M., and Keller, R (1992) Circular DNA molecules
imaged in air by scanning force microscopy Biochemistry 31(1), 22–26.
Bustamante, C., Zuccheri, G., Leuba, S H., Yang, G., and Samor`ı, B (1997) Visualization and analysis of
chromatin by scanning force microscopy Methods—A Companion Methods Enzymol 12(1), 73–83.
Calladine, C R., and Drew, H R (1992) “Understanding DNA : The molecule and How it works.” Academic Press, San Diego, London
Cherny, D I., Fourcade, A., Svinarchuk, F., Nielsen, P E., Malvy, C., and Delain, E (1998) Analysis of
various sequence-specific triplexes by electron and atomic force microscopies Biophys J 74(2 Pt 1), 1015–
1023
Trang 5Cheung, C L., Hafner, J H., and Lieber, C M (2000) Carbon nanotube atomic force microscopy tips: direct
growth by chemical vapor deposition and application to high-resolution imaging Proc Natl Acad Sci.
U.S.A 97(8), 3809–3813.
Clausen-Schaumann, H., Rief, M., Tolksdorf, C., and Gaub, H E (2000) Mechanical stability of single DNA
molecules Biophys J 78(4), 1997–2007.
Coury, J E., Anderson, J R., McFail-Isom, L., Williams, L D., and Bottomley, L A (1997) Scanning force microscopy of small ligand-nucleic acid complexes: Tris(o-phenanthroline)ruthenium(II) as a test for a new
assay J Am Chem Soc 119, 3792–3796.
Coury, J E., McFail-Isom, L., Williams, L D., and Bottomley, L A (1996) A novel assay for drug-DNA
binding mode, affinity, and exclusion number: scanning force microscopy Proc Natl Acad Sci U.S.A.
93(22), 12,283–12,286.
Cozzarelli, N R., Boles, T C., White, J H., and Cozzarelli (1990) Primer on the topology and geometry of
DNA supercoiling In “DNA Topology and Its Biological Effects” (N R Cozzarelli and J C Wang, eds.),
pp 139–215 CSH Laboratory Press, Cold Spring Harbor, NY
Crothers, D M (1998) DNA curvature and deformation in protein-DNA complexes: A step in the right
direction [comment] Proc Natl Acad Sci U.S.A 95(26), 15,163–15,165.
Crothers, D M., Drak, J., Kahn, J D., and Levene, S D (1992) DNA bending, flexibility, and helical repeat
by cyclization kinetics Methods in Enzymology 212, 3–29.
Dai, H., Hafner, J H., Rinzler, A G., Colbert, D T., and Smalley, R E (1996) Nanotubes as nanoprobes in
scanning probe microscopy Nature 384, 147–150.
Dame, R T., Wyman, C., and Goosen, N (2000) H-NS mediated compaction of DNA visualized by atomic
force microscopy Nucl Acids Res 28(18),
Davenport, R J., Wuite, G J., Landick, R., and Bustamante, C (2000) Single-molecule study of transcriptional
pausing and arrest by E coli RNA polymerase [see comments] Science 287(5462), 2497–2500.
Diau, E W G., Herek, J L., Kim, Z H., and Zewail, A H (1998) Femtosecond activation of reactions and
the concept of nonergodic molecules Science 279(5352), 847–851.
Dubochet, J., Adrian, M., Dustin, I., Furrer, P., and Stasiak, A (1992) Cryoelectron microscopy of DNA
molecules in solution Methods in Enzymology 211, 507–518.
Dustin, I., Furrer, P., Stasiak, A., Dubochet, J., Langowski, J., and Egelman, E (1991) Spatial visualization
of DNA in solution J Struct Biol 107(1), 15–21.
Erie, D A., Yang, G., Schultz, H C., and Bustamante, C (1994) DNA bending by Cro protein in specific
and nonspecific complexes: implications for protein site recognition and specificity Science 266(5190),
1562–1566
Fang, Y., and Hoh, J H (1998) Surface-directed DNA condensation in the absence of soluble multivalent
cations Nucl Acids Res 26(2), 588–593.
Fang, Y., and Hoh, J H (1999) Cationic silanes stabilize intermediates in DNA condensation FEBS Lett.
459(2), 173–176.
Fang, Y., Spisz, T S., and Hoh, J H (1999) Ethanol-induced structural transitions of DNA on mica Nucl.
Acids Res 27(8), 1943–1949.
Fang, Y., Spisz, T S., Wiltshire, T., D’Costa, N P., Bankman, I N., Reeves, R H., and Hoh, J H (1998)
Solid-state DNA sizing by atomic force microscopy Anal Chem 70(10), 2123–2129.
Feng, X Z., Bash, R., Balagurumoorthy, P., Lohr, D., Harrington, R E., and Lindsay, S M (2000)
Confor-mational transition in DNA on a cold surface Nucl Acids Res 28(2), 593–596.
Fritzsche, W., Schaper, A., and Jovin, T M (1995) Scanning force microscopy of chromatin fibers in air and
in liquid Scanning 17(3), 148–155.
Frontali, C (1988) Excluded-volume effect on the bidimensional conformation of DNA molecules adsorbed
to protein films Biopolymers 27(8), 1329–1331.
Frontali, C., Dore, E., Ferrauto, A., Gratton, E., Bettini, A., Pozzan, M R., and Valdevit, E (1979) An absolute method for the determination of the persistence length of native DNA from electron micrographs
Biopolymers 18(6), 1353–1373.
Furrer, P., Bednar, J., Stasiak, A Z., Katritch, V., Michoud, D., Stasiak, A., and Dubochet, J (1997) Opposite
effect of counterions on the persistence length of nicked and non-nicked DNA J Mol Biol 266(4), 711–721.
Trang 6Gebe, J A., Delrow, J J., Heath, P J., Fujimoto, B S., Stewart, D W., and Schurr, J M (1996) Effects
of Na+and Mg2 +on the structures of supercoiled DNAs: Comparison of simulations with experiments.
J Mol Biol 262(2), 105–128.
Guthold, M., Zhu, X., Rivetti, C., Yang, G., Thomson, N H., Kasas, S., Hansma, H G., Smith, B., Hansma,
P K., and Bustamante, C (1999) Direct observation of one-dimensional diffusion and transcription by
Escherichia coli RNA polymerase Biophys J 77(4), 2284–2294.
Hafner, J H., Cheung, C L., and Lieber, C M (1999) Direct growth of single-walled carbon nanotube
scanning probe microscopy tips J Am Chem Soc 121, 9750–9751.
Han, W., Dlakic, M., Zhu, Y J., Lindsay, S M., and Harrington, R E (1997) Strained DNA is kinked by low concentrations of Zn2+ Proc Natl Acad Sci U.S.A 94(20), 10,565–10,570.
Han, W., Lindsay, S M., Dlakic, M., and Harrington, R E (1997) Kinked DNA [letter] Nature 386(6625),
563
Hansma, H G., Bezanilla, M., Zenhausern, F., Adrian, M., and Sinsheimer, R L (1993) Atomic force
microscopy of DNA in aqueous solutions Nucl Acids Res 21(3), 505–512.
Hansma, P K., Cleveland, J P., Radmacher, M., Walters, D A., Hillner, P E., Bezanilla, M., Fritz, M., Vie, D., Hansma, H G., Prater, C B., Massie, J., Fukunaga, L., Gurley, J., and Elings, V (1994) Tapping mode
atomic force microscopy in liquids Appl Phys Lett 64(13), 1738–1740.
Hansma, H., Golan, R., Hsieh, W., Daubendiek, S L., and Kool, E T (1999) Polymerase Activities and RNA
Structures in the Atomic Force Microscope J Struct Biol 127, 240–247.
Hansma, H G., and Laney, D E (1996) DNA binding to mica correlates with cationic radius: Assay by
atomic force microscopy Biophys J 70(4), 1933–1939.
Hansma, H G., Laney, D E., Bezanilla, M., Sinsheimer, R L., and Hansma, P K (1995) Applications for
atomic force microscopy of DNA Biophys J 68(5), 1672–1677.
Hansma, H G., Revenko, I., Kim, K., and Laney, D E (1996) Atomic force microscopy of long and short
double-stranded, single-stranded and triple-stranded nucleic acids Nucl Acids Res 24(4), 713–720.
Hansma, H G., Sinsheimer, R L., Li, M Q., and Hansma, P K (1992) Atomic force microscopy of
single-and double-strsingle-anded DNA Nucl Acids Res 20(14), 3585–3590.
Hansma, H G., Vesenka, J., Siegerist, C., Kelderman, G., Morrett, H., Sinsheimer, R O., Elings, V., Bustamante, C., and Hansma, P K (1992) Reproducible imaging and dissection of plasmid DNA under liquid with the
atomic force microscope Science 256(5060), 1180 –1184.
Heckl, W M (1998) The combination of AFM Nanodissection with PCR BIOforum Int 2, 133–138.
Hegner, M., Wagner, P., and Semenza, G (1993) Immobilizing DNA on gold via thiol modification for atomic
force microscopy imaging in buffer solutions FEBS Lett 336(3), 452– 456.
Henderson, E (1992) Imaging and nanodissection of individual supercoiled plasmids by atomic force
mi-croscopy Nucl Acids Res 20(3), 445– 447.
Israelachvili, J N (1992) “Intermolecular and Surface Forces.” Academic Press, London
Jeltsch, A (1998) Flexibility of DNA in complex with proteins deduced from the distribution of bending
angles observed by scanning force microscopy Biophys Chem 74, 53–57.
Ji, X., Oh, J., Dunker, A K., and Hipps, K W (1998) Effects of relative humidity and applied force on atomic
force microscopy images of the filamentous phage fd Ultramicroscopy 72(3– 4), 165–176.
Joanicot, M., and Revet, B (1987) DNA conformational studies from electron microscopy I Excluded volume
effect and structure dimensionality Biopolymers 26(2), 315–326.
Karrasch, S., Dolder, M., Schabert, F., Ramsden, J., and Engel, A (1993) Covalent binding of biological
samples to solid supports for scanning probe microscopy in buffer solution Biophys J 65(6), 2437–
2446
Kasas, S., Thomson, N H., Smith, B L., Hansma, H G., Zhu, X., Guthold, M., Bustamante, C., Kool, E T., Kashlev, M., and Hansma, P K (1997) Escherichia coli RNA polymerase activity observed using atomic
force microscopy Biochemistry 36(3), 461– 468.
Keller, D J., and Chih-Chung, C (1992) Imaging steep, high structures by scanning force microscopy with
electron beam deposited tips Surf Sci 268(1–3), 333–339.
Krylov, D., Makarov, V L., and Ivanov, V I (1990) The B-A transition in superhelical DNA Nucl Acids
Res 18(4), 759–761.
Trang 7Kumar, A., Larsson, O., Parodi, D., and Liang, Z (2000) Silanized nucleic acids: a general platform for DNA
immobilization Nucl Acids Res 28(14), e71.
Lee, G U., Chrisey, L A., and Colton, R J (1994) Direct measurement of the forces between complementary
strands of DNA Science 266(5186), 771–773.
Lindsay, S M., Tao, N J., DeRose, J A., Oden, P I., Lyubchenko, Y L., Harrington, R E., and Shlyakhtenko,
L (1992) Potentiostatic deposition of DNA for scanning probe microscopy Biophys J 61(6), 1570 –
1584
Lyubchenko, Y L., Gall, A A., Shlyakhtenko, L S., Harrington, R E., Jacobs, B L., Oden, P I., and Lindsay,
S M (1992) Atomic force microscopy imaging of double stranded DNA and RNA J Biomol Struct Dyn.
10(3), 589–606.
Lyubchenko, Y L., Jacobs, B L., and Lindsay, S M (1992) Atomic force microscopy of reovirus dsRNA: A
routine technique for length measurements Nucl Acids Res 20(15), 3983–3986.
Lyubchenko, Y L., and Shlyakhtenko, L S (1997) Visualization of supercoiled DNA with atomic force
microscopy in situ Proc Natl Acad Sci U.S.A 94(2), 496 –501.
Mou, J., Czajkowsky, D M., Zhang, Y., and Shao, Z (1995) High-resolution atomic-force microscopy of
DNA: the pitch of the double helix FEBS Lett 371(3), 279–282.
Murakami, M., Hirokawa, H., and Hayata, I (2000) Analysis of radiation damage of DNA by atomic force
microscopy in comparison with agarose gel electrophoresis J Biochem Biophys Methods 44, 31– 40.
Murray, M N., Hansma, H G., Bezanilla, M., Sano, T., Ogletree, D F., Kolbe, W., Smith, C L., Cantor, C R., Spengler, S., Hansma, P K., and Salmeron, M (1993) Atomic force microscopy of biochemically tagged
DNA Proc Natl Acad Sci U.S.A 90(9), 3811–3814.
Muzard, G., Theveny, B., and Revet, B (1990) Electron microscopy mapping of pBR322 DNA curvature
Comparison with theoretical models EMBO J 9(4), 1289–1298.
Muzzalupo, I., Nigro, C., Zuccheri, G., Samor`ı, B., Quagliariello, C., and Buttinelli, M (1995) Deposition
on mica and scanning force microscopy imaging of DNA molecules whose original B structure is retained
J Vacuum Sci Technol A (Vacuum, Surfaces, and Films) 13(3, pt 2), 1752–1754.
Nishimura, S., Biggs, S., Scales, P J., Healy, T W., Tsunematsu, K., and Tateyama, T (1994) Molecular-scale
structure of the cation modified muscovite mica masal plane Langmuir 10(12), 4554– 4559.
Nishimura, S., Scales, P J., Tateyama, H., Tsunematsu, K., and Healy, T W (1995) Cationic modification of
muscovite mica - an electrokinetic study Langmuir 11(1), 291–295.
Noy, A., Vezenov, D V., Kayyem, J F., Meade, T J., and Lieber, C M (1997) Stretching and breaking duplex
DNA by chemical force microscopy Chem Biol 4(7), 519–527.
Oussatcheva, E A., Shlyakhtenko, L S., Glass, R., Sinden, R R., Lyubchenko, Y L., and Potaman, V N
(1999) Structure of branched DNA molecules: gel retardation and atomic force microscopy studies J Mol.
Biol 292(1), 75–86.
Paige, C R., Kornicker, W A., Hileman, O E., and Snodgrass, W J (1992) Kinetics of desorption of ions
from quartz and mica surfaces J Radioanal Nucl Chem Art 159, 37– 46.
Pietrasanta, L I., Schaper, A., and Jovin, T M (1994) Probing specific molecular conformations with the
scanning force Nucl Acids Res 22(16), 3288–3292.
Pope, L H., Davies, M C., Laughton, C A., Roberts, C J., Tendler, S J., and Williams, P M (1999) Intercalation-induced changes in DNA supercoiling observed in real-time by atomic force microscopy
Anal Chim Acta 400, 27–32.
Pope, L H., Davies, M C., Laughton, C A., Roberts, C J., Tendler, S J., and Williams, P M (2000) Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure [In Process
Citation] J Microsc 199(Pt 1), 68–78.
Putman, C A J., van der Werf, K O., de Grooth, B G., and van Hulst, N F (1994) Tapping mode atomic
force microscopy in liquid Appl Phys Lett 64(18), 2454 –2456.
Rabke, C E., Wenzler, L A., and Beebe, T P Jr (1994) Electron spectroscopy and atomic force microscopy
studies of DNA adsorption on mica Scan Microsc 8(3), 471– 480.
Ramachandran, T R., Madhukar, A., Chen, P., and Koel, B E (1998) Imaging and direct manipulation of
nanoscale three-dimensional features using the noncontact atomic force microscope J Vacuum Sci Technol.
A (Vacuum, Surfaces, and Films) 16(3), 1425–1429.
Trang 8Rippe, K., Guthold, M., von Hippel, P H., and Bustamante, C (1997) Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E coli RNA polymerase× sigma 54
holoenzyme by scanning force microscopy J Mol Biol 270(2), 125–138.
Rippe, K., M¨ucke, N., and Langowski, J (1997) Superhelix dimensions of a 1868 base pair plasmid determined
by scanning force microscopy in air and in acqueous solution Nucl Acids Res 25(9), 1736–1744.
Rivetti, C., and Codeluppi, S (2001) Accurate length determination of DNA molecules visualized by atomic
force microscopy: Evidence for a partial B- to A-form transition on mica Ultramicroscopy 87(1–2), 55–66.
Rivetti, C., Guthold, M., and Bustamante, C (1996) Scanning force microscopy of DNA deposited onto mica:
equilibration versus kinetic trapping studied by statistical polymer chain analysis J Mol Biol 264(5),
919–932
Rivetti, C., Guthold, M., and Bustamante, C (1999) Wrapping of DNA around the E coli RNA polymerase
open promoter complex EMBO J 18(16), 4464 – 4475.
Rivetti, C., Walker, C., and Bustamante, C (1998) Polymer chain statistics and conformational analysis of
DNA molecules with bends or sections of different flexibility J Mol Biol 280(1), 41–59.
Samor`ı, B (1998) Stretching, tearing, and dissecting single molecules of DNA Angew Chem Int Ed 37(16),
2198–2200
Samor`ı, B., Muzzalupo, I., and Zuccheri, G (1996) Deposition of supercoiled DNA on mica for scanning
force microscopy imaging Scan Microsc 10(4), 953–962.
Samor`ı, B., Nigro, C., Armentano, V., Cimieri, S., Zuccheri, G., and Quagliariello, C (1993) DNA supercoiling
imaged in 3 Dimensions by scanning force microscopy Angew Chem Int Ed 32(10), 1461–1463.
Schaper, A., Pietrasanta, L I., and Jovin, T M (1993) Scanning force microscopy of circular and linear
plasmid DNA spread on mica with a quaternary ammonium salt Nucl Acids Res 21, 6004 –6009.
Schepartz, A (1995) Nonspecific DNA bending and the specificity of protein-DNA interactions Science
269(5226), 989–990.
Shlyakhtenko, L S., Gall, A A., Weimer, J J., Hawn, D D., and Lyubchenko, Y L (1999) Atomic force
microscopy imaging of DNA covalently immobilized on a functionalized mica surface Biophys J 77,
568–576
Shlyakhtenko, L S., Potaman, V N., Sinden, R R., Gall, A A., and Lyubchenko, Y L (2000) Structure and
dynamics of three-way DNA junctions: atomic force microscopy studies Nucl Acids Res 28(18), 34–72.
Shpigelman, E S., Trifonov, E N., and Bolshoy, A (1993) Curvature—Software for the analysis of curved
DNA CABIOS 9(4), 435– 440.
Spisz, T S., Fang, Y., Reeves, R H., Seymour, C K., Bankman, I N., and Hoh, J H (1998) Automated sizing
of DNA fragments in atomic force microscope images Med Biol Eng Comput 36(6), 667–672.
Steinberg, I Z (1994) Brownian motion of the end-to-end distance in oligopeptide molecules: Numerical
solution of the diffusion equations as coupled first order linear differential equations J Theor Biol 166(2),
173–187
Strother, T., Hamers, R J., and Smith, L M (2000) Covalent attachment of oligodeoxyribonucleotides to
amine-modified Si (001) surfaces Nucl Acids Res 28(18), 3535–3541.
Strunz, T., Hegner, M., Oroszlan, K., Schumakovic, I., and G¨untherdt, H.-J (2000) Force spectroscopy and
dissociation kinetics of single molecules under an applied force Single Mol 1(2), 175.
Strunz, T., Oroszlan, K., Schafer, R., and Guntherodt, H J (1999) Dynamic force spectroscopy of single
DNA molecules Proc Natl Acad Sci U.S.A 96(20), 11,277–11,282.
Thalhammer, S., Stark, R W., Muller, S., Wienberg, J., and Heckl, W M (1997) The atomic force microscope
as a new microdissecting tool for the generation of genetic probes J Struct Biol 119(2), 232–237.
Theveny, B., and Revet, B (1987) DNA orientation using specific avidin-ferritin biotin end labelling Nucl.
Acids Res 15(3), 947–958.
Thundat, T., Allison, D P., Warmack, R J., and Ferrell, T L (1992) Imaging isolated strands of DNA
molecules by atomic force microscopy Ultramicroscopy 42(44, pt.B), 1101–1106.
Thundat, T., Warmack, R J., Allison, D P., Bottomley, L A., Lourenco, A J., and Ferrell, T L (1992) Atomic force microscopy of deoxyribonucleic acid strands adsorbed on mica: The effect of humidity on apparent
width and image contrast J Vacuum Sci Technol A (Vacuum, Surfaces, and Films) 10(4, pt 1), 630 –
635
Trang 9Thundat, T., Zheng, X Y., Chen, G Y., and Warmack, R J (1993) Role of relative humidity in atomic force
microscopy imaging Surf Sci 294(1,2), L939–L943.
van Noort, S J., van Der Werf, K O., de Grooth, B G., and Greve, J (1999) High speed atomic force
microscopy of biomolecules by image tracking Biophys J 77(4), 2295–2303.
van Noort, S J., van der Werf, K O., Eker, A P., Wyman, C., de Grooth, B G., van Hulst, N F., and Greve, J (1998) Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope
[see comments] Biophys J 74(6), 2840 –2849.
Vesenka, J., Guthold, M., Tang, C L., Keller, D., Delaine, E., and Bustamante, C (1992) Substrate preparation
for reliable imaging of DNA molecules with the scanning force microscope Ultramicroscopy 42(44, pt B),
1243–1249
Vesenka, J., Manne, S., Yang, G., Bustamante, C J., and Henderson, E (1993) Humidity effects on atomic
force microscopy of gold-labeled DNA on mica Scan Microsc 7(3), 781–788.
Vologodskii, A V (1992) “Topology and Physics of Circular DNA.” CRC Press, Boca Raton, FL Vologodskii, A V., and Cozzarelli, N R (1994) Conformational and thermodynamic properties of supercoiled
DNA Annu Rev Biophys Biomol Struct 23, 609–643.
Wagner, P., Nock, S., Spudich, J A., Volkmuth, W D., Chu, S., Cicero, R L., Wade, C P., Linford, M R., and Chidsey, C E (1997) Bioreactive self-assembled monolayers on hydrogen-passivated Si(111) as a
new class of atomically flat substrates for biological scanning probe microscopy J Struct Biol 119(2),
189–201
Weisenhorn, A L., Egger, M., Ohnesorge, F., Gould, S A C., Heyn, S.-P., Hansma, H G., Sinsheimer, R L., Gaub, H E., and Hansma, P K (1991) Molecular-resolution images of Langmuir-Blodgett and DNA by
atomic force microscopy Langmuir 7, 8–12.
Weisenhorn, A L., Gaub, H E., Hansma, H G., Sinsheimer, R L., Kelderman, G L., and Hansma, P K (1990) Imaging single-stranded DNA, antigen-antibody reaction and polymerized langmuir-blodgett films
with an atomic force microscope Scan Microsc 4(3), 511–516.
White, J H (1989) An introduction to the geometry and topology of DNA structure In “Mathematical
Methods for DNA Sequences,” pp 225–253 CRC Press, Boca Raton, FL
Wong, S S., Harper, J D., Lansbury, P T., and Lieber, C M (1998) Carbon nanotube tips: High-resolution
probes for imaging biological systems J Am Chem Soc 120(3), 603–604.
Wong, S S., Joselevich, E., Woolley, A T., Cheung, C L., and Lieber, C M (1998) Covalently functionalized
nanotubes as nanometre-sized probes in chemistry and biology Nature 394(6688), 52–55.
Wyman, C., Rombel, I., North, A K., Bustamante, C., and Kustu, S (1997) Unusual oligomerization
re-quired for activity of NtrC, a bacterial enhancer-binding protein [see comments] Science 275(5306), 1658–
1661
Xu, Y C., and Bremer, H (1997) Winding of the DNA helix by divalent metal ions Nucl Acids Res 25(20),
4067– 4071
Xu, X M., and Ikai, A (1998) 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
Biochem Biophys Res Commun 248(3), 744 –748.
Yang, J., and Shao, Z (1993) Effect of probe force on the resolution of atomic force microscopy of DNA
Ultramicroscopy 50(2), 157–170.
Yang, J., Takeyasu, K., and Shao, Z (1992) Atomic force microscopy of DNA molecules FEBS Lett 301(2),
173–176
Yang, G., Vesenka, J P., and Bustamante, C J (1996) Effects of tip-sample forces and humidity on the imaging
of DNA with a scanning force microscope Scanning 18(5), 344–350.
Yoshimura, S H., Ohniwa, R L., Sato, M H., Matsunaga, F., Kobayashi, G., Uga, H., Wada, C., and Takeyasu,
K (2000) DNA phase transition promoted by replication initiator Biochemistry 39(31), 9139–9145.
Zenhausern, F., Adrian, M., Ten Heggeler-Bordier, B., Emch, R., Jobin, M., Taborelli, M., and Descouts, P
(1992) Imaging of DNA by scanning force microscopy J Struct Biol 108(1), 69–73.
Zenhausern, F., Adrian, M., Ten Heggeler-Bordier, B., Eng, L M., and Descouts, P (1992) DNA and RNA polymerase/DNA complex imaged by scanning force microscopy: influence of molecular-scale friction
Scanning 14(4), 212–217.
Trang 10Zenhausern, F., Eng, L M., Adrian, M., Kasas, S., Weisenhorn, A L., and Descouts, P (1992) A scanning
force microscopy investigation of DNA adsorbed on mica Helv Phys Acta 65(6), 820 –821.
Zuccheri, G., Bergia, A., Gallinella, G., Musiani, M., and Samor`ı, B (2000) Scanning force microscopy study
on a single-stranded DNA: the genome of Parvovirus B19 Chem Bio Chem 2(3), 199–204.
Zuccheri, G., Dame, R T., Aquila, M., Muzzalupo, I., and Samor`ı, B (1998) Conformational
fluctua-tions of supercoiled DNA molecules observed in real time with a scanning force microscope Appl Phys.
A 66(suppl., pt 1–2), S585–S589.
Zuccheri, G., Scipioni, A., Cavaliere, V., Gargiulo, G., De Santis, P., and Samor`ı, B (2001) Mapping the
instrinsic curvature and flexibility along the DNA chain Proc Natl Acad Sci U.S.A 98(6), 3074–3079.