Circular DNA molecules imaged in air by scanning force microscopy.

Routine and reproducible imaging of DNA molecules in air with the scanning force microscope (SFM) has been accomplished. Circular molecules of plasmid DNA were deposited onto red mica and imaged under various relative humidities. In related experiments, the first images of the Escherichia coli RNA polymerase-DNA complex have also been obtained. This has been possible by (1) the use of specially modified SFM tips with a consistent radius of curvature of 10 nm or less, to minimize the amount of image distortion introduced by the finite dimensions of commercially available tips, (2) the optimization of a method to deposit and bind DNA molecules to the mica surface in a stable fashion, and (3) careful control of the sample humidity, to prevent solvation of the molecules and detachment from the surface by the scanning tip or stylus. Contact forces in the range of a few nanonewtons are routinely possible in air and in the presence of residual humidity. The spatial resolution of the images appears determined by the radius of curvature of the modified styli, which can be estimated directly from the apparent widths of the DNA molecules in the images.

[1]  E. Clementi,et al.  Interaction of Water with DNA Single‐Helix in the A Conformation , 1979, Biopolymers.

[2]  J. Brahms,et al.  Dependence of B-A conformational change in DNA on base composition. , 1972, Nature: New biology.

[3]  D. Lazinski,et al.  Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif , 1989, Cell.

[4]  H. Murakami,et al.  New scanning tunneling microscopy tip for measuring surface topography , 1990 .

[5]  Galen D. Stucky,et al.  Progress in sequencing deoxyribonucleic acid with an atomic force microscope , 1991 .

[6]  J. Hearst.  Determination of the dominant factors which influence the net hydration of native sodium deoxyribonucleate , 1965 .

[7]  E. Clementi,et al.  Simulations of the solvent structure for macromolecules. I. Solvation of B‐DNA double helix at T = 300 K , 1981 .

[8]  K. L. Lee,et al.  Direct electron‐beam patterning for nanolithography , 1989 .

[9]  T. Thundat,et al.  STM and AFM images of nucleosome DNA under water. , 1989, Journal of biomolecular structure & dynamics.

[10]  K. A. Hartman,et al.  Hydration of Deoxyribonucleic Acid. II. An Infrared Study , 1963 .

[11]  K. A. Hartman,et al.  Hydration of Deoxyribonucleic Acid. I. a Gravimetric Study , 1962 .

[12]  A Engel,et al.  Biological applications of scanning probe microscopes. , 1991, Annual review of biophysics and biophysical chemistry.

[13]  G. McFadden,et al.  Replication and resolution of cloned poxvirus telomeres in vivo generates linear minichromosomes with intact viral hairpin termini , 1986, Journal of virology.

[14]  J. Hearst,et al.  The net hydration of deoxyribonucleic acid. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Quate,et al.  Forces in atomic force microscopy in air and water , 1989 .

[16]  B. Persson.  The atomic force microscope: Can it be used to study biological molecules? , 1987 .

[17]  Enrico Clementi,et al.  A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T=300 K , 1980 .

[18]  J. M. Drake,et al.  Special Issue: Dynamics of Molecular Systems , 1990 .

[19]  M. Chamberlin,et al.  Isolation and properties of transcribing ternary complexes of Escherichia coli RNA polymerase positioned at a single template base. , 1987, Journal of molecular biology.

[20]  P K Hansma,et al.  Atomic force microscopy of hydrated phosphatidylethanolamine bilayers. , 1991, Biophysical journal.

[21]  A. Das,et al.  NusA protein is necessary and sufficient in vitro for phage lambda N gene product to suppress a rho-independent terminator placed downstream of nutL. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[22]  P. Hansma,et al.  Scanning tunneling microscopy and atomic force microscopy: application to biology and technology. , 1988, Science.

[23]  S. Hanlon,et al.  Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration. , 1975, Biochemistry.