Abstract
The dynamics and enzymatic degradation of single DNA molecules can now be observed with the atomic force microscope. A combination of two advances has made this possible. Tapping in fluid has reduced lateral forces, which permits the imaging of loosely adsorbed molecules; and the presence of nickel ions appears to form a relatively stable bridge between the negatively charged mica and the negatively charged DNA phosphate backbone. Continuous imaging shows DNA motion and the process of DNA degradation by the nuclease DNase I. It is possible to see DNase degradation of both loosely adsorbed and tightly adsorbed DNA molecules. This method gives images in aqueous buffer of bare, uncoated DNA molecules with lengths of only a few hundred base pairs, or approximately 100 nm in length.
Full text
PDF![2454](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/418615e8b279/biophysj00068-0328.png)
![2455](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/709ad7d01cb7/biophysj00068-0329.png)
![2456](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/382335371c96/biophysj00068-0330.png)
![2457](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/f70f571f09a5/biophysj00068-0331.png)
![2458](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/16f3295aec98/biophysj00068-0332.png)
![2459](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2503/1225630/8091b7bdb112/biophysj00068-0333.png)
Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Binnig G, Quate CF, Gerber C. Atomic force microscope. Phys Rev Lett. 1986 Mar 3;56(9):930–933. doi: 10.1103/PhysRevLett.56.930. [DOI] [PubMed] [Google Scholar]
- Bustamante C. Direct observation and manipulation of single DNA molecules using fluorescence microscopy. Annu Rev Biophys Biophys Chem. 1991;20:415–446. doi: 10.1146/annurev.bb.20.060191.002215. [DOI] [PubMed] [Google Scholar]
- Bustamante C., Vesenka J., Tang C. L., Rees W., Guthold M., Keller R. Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry. 1992 Jan 14;31(1):22–26. doi: 10.1021/bi00116a005. [DOI] [PubMed] [Google Scholar]
- Gurrieri S., Rizzarelli E., Beach D., Bustamante C. Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy. Biochemistry. 1990 Apr 3;29(13):3396–3401. doi: 10.1021/bi00465a036. [DOI] [PubMed] [Google Scholar]
- Hansma H. G., Bezanilla M., Zenhausern F., Adrian M., Sinsheimer R. L. Atomic force microscopy of DNA in aqueous solutions. Nucleic Acids Res. 1993 Feb 11;21(3):505–512. doi: 10.1093/nar/21.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hansma H. G., Sinsheimer R. L., Groppe J., Bruice T. C., Elings V., Gurley G., Bezanilla M., Mastrangelo I. A., Hough P. V., Hansma P. K. Recent advances in atomic force microscopy of DNA. Scanning. 1993 Sep-Oct;15(5):296–299. doi: 10.1002/sca.4950150509. [DOI] [PubMed] [Google Scholar]
- Hansma H. G., Vesenka J., Siegerist C., Kelderman G., Morrett H., Sinsheimer R. L., Elings V., Bustamante C., Hansma P. K. Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope. Science. 1992 May 22;256(5060):1180–1184. doi: 10.1126/science.256.5060.1180. [DOI] [PubMed] [Google Scholar]
- Ill C. R., Keivens V. M., Hale J. E., Nakamura K. K., Jue R. A., Cheng S., Melcher E. D., Drake B., Smith M. C. A COOH-terminal peptide confers regiospecific orientation and facilitates atomic force microscopy of an IgG1. Biophys J. 1993 Mar;64(3):919–924. doi: 10.1016/S0006-3495(93)81452-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kashlev M., Martin E., Polyakov A., Severinov K., Nikiforov V., Goldfarb A. Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme. Gene. 1993 Aug 16;130(1):9–14. doi: 10.1016/0378-1119(93)90340-9. [DOI] [PubMed] [Google Scholar]
- Kuriyan J., O'Donnell M. Sliding clamps of DNA polymerases. J Mol Biol. 1993 Dec 20;234(4):915–925. doi: 10.1006/jmbi.1993.1644. [DOI] [PubMed] [Google Scholar]
- Lyubchenko Y. L., Gall A. A., Shlyakhtenko L. S., Harrington R. E., Jacobs B. L., Oden P. I., Lindsay S. M. Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn. 1992 Dec;10(3):589–606. doi: 10.1080/07391102.1992.10508670. [DOI] [PubMed] [Google Scholar]
- Lyubchenko Y. L., Oden P. I., Lampner D., Lindsay S. M., Dunker K. A. Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. Nucleic Acids Res. 1993 Mar 11;21(5):1117–1123. doi: 10.1093/nar/21.5.1117. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lyubchenko Y., Shlyakhtenko L., Harrington R., Oden P., Lindsay S. Atomic force microscopy of long DNA: imaging in air and under water. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2137–2140. doi: 10.1073/pnas.90.6.2137. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Perkins T. T., Quake S. R., Smith D. E., Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science. 1994 May 6;264(5160):822–826. doi: 10.1126/science.8171336. [DOI] [PubMed] [Google Scholar]
- Perkins T. T., Smith D. E., Chu S. Direct observation of tube-like motion of a single polymer chain. Science. 1994 May 6;264(5160):819–822. doi: 10.1126/science.8171335. [DOI] [PubMed] [Google Scholar]
- Rhodes D., Klug A. Helical periodicity of DNA determined by enzyme digestion. Nature. 1980 Aug 7;286(5773):573–578. doi: 10.1038/286573a0. [DOI] [PubMed] [Google Scholar]
- Schwartz D. C., Li X., Hernandez L. I., Ramnarain S. P., Huff E. J., Wang Y. K. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science. 1993 Oct 1;262(5130):110–114. doi: 10.1126/science.8211116. [DOI] [PubMed] [Google Scholar]
- Snow E. T., Xu L. S., Kinney P. L. Effects of nickel ions on polymerase activity and fidelity during DNA replication in vitro. Chem Biol Interact. 1993 Sep;88(2-3):155–173. doi: 10.1016/0009-2797(93)90089-h. [DOI] [PubMed] [Google Scholar]
- Suck D., Oefner C. Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA. Nature. 1986 Jun 5;321(6070):620–625. doi: 10.1038/321620a0. [DOI] [PubMed] [Google Scholar]
- Thundat T., Allison D. P., Warmack R. J., Brown G. M., Jacobson K. B., Schrick J. J., Ferrell T. L. Atomic force microscopy of DNA on mica and chemically modified mica. Scanning Microsc. 1992 Dec;6(4):911–918. [PubMed] [Google Scholar]
- Vesenka J., Guthold M., Tang C. L., Keller D., Delaine E., Bustamante C. Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy. 1992 Jul;42-44(Pt B):1243–1249. doi: 10.1016/0304-3991(92)90430-r. [DOI] [PubMed] [Google Scholar]
- Volkmuth W. D., Austin R. H. DNA electrophoresis in microlithographic arrays. Nature. 1992 Aug 13;358(6387):600–602. doi: 10.1038/358600a0. [DOI] [PubMed] [Google Scholar]
- von Hippel P. H. Protein-DNA recognition: new perspectives and underlying themes. Science. 1994 Feb 11;263(5148):769–770. doi: 10.1126/science.8303292. [DOI] [PubMed] [Google Scholar]