DNA height in scanning force microscopy.

The measured height of DNA molecules adsorbed on a mica substrate by scanning probe microscopy is always less than the theoretical diameter. In this paper we show that, when imaged in ambient conditions, the molecules are usually immersed in the salt layer used to adsorb them to the substrate. This layer distorts the measurement of DNA height and is the main source of error but not the only one. We have performed different experiments to study this problem using two scanning force techniques: non-contact tapping mode in air and jumping mode in aqueous solution, where the dehydration phenomena is minimized. Height measurements of DNA in air using tapping mode reveal a height of 0.7+/-0.2nm. This value increases up to 1.5+/-0.2nm when the salt layer, in which the molecules are embedded, is removed. Jumping experiments in water give a value of 1.4+/-0.3nm when the maximum applied force is 300pN and 1.8+/-0.2nm at very low forces, which confirms the removal of the salt layer. Still, in all our experiments, the measured height of the DNA is less than the theoretical value. Our results show that although the salt layer present is important, some sample deformation due to either the loading force of the tip or the interaction with the substrate is also present.

[1]  Y. Lyubchenko,et al.  Atomic force microscopic demonstration of DNA looping by GalR and HU. , 1997, Nucleic acids research.

[2]  Jan Greve,et al.  Tapping mode atomic force microscopy in liquid , 1994 .

[3]  Y. Lyubchenko,et al.  Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. , 1993, Nucleic acids research.

[4]  A. Baró,et al.  Intermittent contact scanning force microscopy: The role of the liquid necks , 1998 .

[5]  Miss A.O. Penney.  (b) , 1974, The New Yale Book of Quotations.

[6]  David Keller,et al.  Biochemical and structural applications of scanning force microscopy , 1994 .

[7]  P K Hansma,et al.  Escherichia coli RNA polymerase activity observed using atomic force microscopy. , 1997, Biochemistry.

[8]  A. Engel,et al.  High resolution imaging of native biological sample surfaces using scanning probe microscopy. , 1997, Current opinion in structural biology.

[9]  David Keller,et al.  Scanning force microscopy of nucleic acids and nucleoprotein assemblies , 1993 .

[10]  M. Ishikawa,et al.  Atomic force microscopy of DNA molecules stretched by spin-coating technique. , 2000, Analytical biochemistry.

[11]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[12]  D. Keller,et al.  Scanning force microscopy under aqueous solutions. , 1997, Current opinion in structural biology.

[13]  Wen-Ling Shaiu,et al.  Atomic force microscopy of oriented linear DNA molecules labeled with 5nm gold spheres , 1993, Nucleic Acids Res..

[14]  T. Kawai,et al.  Observation of single- and double-stranded DNA using non-contact atomic force microscopy , 1999 .

[15]  Z. Shao,et al.  Effect of probe force on the resolution of atomic force microscopy of DNA. , 1993, Ultramicroscopy.

[16]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[17]  A M Baró,et al.  Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy. , 2001, Biochemical and biophysical research communications.

[18]  M. Saraste,et al.  FEBS Lett , 2000 .

[19]  H. Hansma,et al.  Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. , 1996, Nucleic acids research.

[20]  Y. Lyubchenko,et al.  Atomic force microscopy of long DNA: imaging in air and under water. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  C. Bustamante,et al.  Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. , 1992, Ultramicroscopy.

[22]  H. Güntherodt,et al.  Dynamic force microscopy in liquids , 1994 .

[23]  C. Bustamante,et al.  Circular DNA molecules imaged in air by scanning force microscopy. , 1992, Biochemistry.

[24]  Paul K. Hansma,et al.  Tapping mode atomic force microscopy in liquids , 1994 .

[25]  Y. Lyubchenko,et al.  Atomic force microscopy imaging of double stranded DNA and RNA. , 1992, Journal of biomolecular structure & dynamics.

[26]  H. Hansma,et al.  Atomic force microscopy of single- and double-stranded DNA. , 1992, Nucleic acids research.

[27]  X. Wallart,et al.  MICROSCOPIC BEHAVIOR OF SILICON IN SILICON DELTA-DOPED LAYER IN GAAS , 1998 .

[28]  A M Baró,et al.  Analysis by atomic force microscopy of Med8 binding to cis‐acting regulatory elements of the SUC2 and HXK2 genes of Saccharomyces cerevisiae , 1999, FEBS letters.

[29]  S. Pongor,et al.  Anisotropic elastic bending models of DNA , 1996 .

[30]  Gerber,et al.  Atomic Force Microscope , 2020, Definitions.

[31]  Julio Gómez-Herrero,et al.  Jumping mode scanning force microscopy , 1998 .

[32]  Andrew G. Glen,et al.  APPL , 2001 .

[33]  Julio Gómez-Herrero,et al.  The role of shear forces in scanning force microscopy: a comparison between the jumping mode and tapping mode , 2000 .

[34]  C. Siegerist,et al.  Reproducible Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic Force Microscope , 1992, Science.

[35]  P. Hansma,et al.  Reversible Binding of DNA to Mica for AFM Imaging , 1996 .

[36]  C. le Grimellec,et al.  Visualization of trp repressor and its complexes with DNA by atomic force microscopy. , 1998, Biophysical journal.

[37]  Sabine Hild,et al.  The simultaneous measurement of elastic, electrostatic and adhesive properties by scanning force microscopy: pulsed-force mode operation , 1997 .

[38]  R. Guckenberger,et al.  STM on Wet Insulators: Electrochemistry or Tunneling? , 1995, Science.

[39]  J. Gómez‐Herrero,et al.  Scanning force microscopy jumping and tapping modes in liquids , 2002 .