Nucleic Acids Research, Vol 24, Issue 4 713-720, Copyright © 1996 by Oxford University Press
HG Hansma, I Revenko, K Kim and DE Laney
Atomic force microscopy (AFM, also called scanning force microscopy) is
proving to be a useful technique for imaging DNA. Thus it is important to
push the limits of AFM imaging in order to explore both what types of DNA
can be reliably imaged and identified and also what substrates and methods
of sample preparation are suitable. The following advances in AFM of DNA
are presented here. (i) DNA molecules as short as 25 bases can be seen by
AFM. The short single-stranded DNAs imaged here (25 and 50 bases long)
appeared globular in the AFM, perhaps because they are all capable of
intramolecular base pairing and because the DNAs were in a Mg(ll) buffer,
which facilitates intramolecular cross- bridging. (ii) AFM images in air of
short double-stranded DNA molecules, 100-200 bp, gave lengths consistent
with A-DNA. (iii) AFM images of poly (A) show both short bent lumpy
molecules with an apparent persistence length of 40 nm and long straight
molecules with an apparent persistence length of 600 nm. For comparison,
the apparent persistence length for double-stranded DNA from phX-174 under
the same conditions was 80 nm. (iv) Structures believed to be triple-
stranded DNA were seen in samples of poly(dA.poly(dT) and poly
(dG).poly(dC). These structures were twice as high as double-stranded DNA
and the same width. (v) Entire molecules of lambda DNA, approx. 16 micron
long, were imaged clearly in overlapping scans. (vi) Plasmid DNA was imaged
on oxidized silicon, although less clearly than on mica.
ARTICLES
Atomic force microscopy of long and short double-stranded, single- stranded and triple-stranded nucleic acids
Department of Physics, University of California, Santa Barbara, 93106, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. A. Forties, R. Bundschuh, and M. G. Poirier The flexibility of locally melted DNA Nucleic Acids Res., August 1, 2009; 37(14): 4580 - 4586. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. E. Alvarez, M. F. Lodeiro, S. J. Luduena, L. I. Pietrasanta, and A. V. Gamarnik Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome J. Virol., June 1, 2005; 79(11): 6631 - 6643. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Kerkmann, L. T. Costa, C. Richter, S. Rothenfusser, J. Battiany, V. Hornung, J. Johnson, S. Englert, T. Ketterer, W. Heckl, et al. Spontaneous Formation of Nucleic Acid-based Nanoparticles Is Responsible for High Interferon-{alpha} Induction by CpG-A in Plasmacytoid Dendritic Cells J. Biol. Chem., March 4, 2005; 280(9): 8086 - 8093. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. S. Andersen, S. A. Contera, B. Knudsen, C. K. Damgaard, F. Besenbacher, and J. Kjems Role of the Trans-activation Response Element in Dimerization of HIV-1 RNA J. Biol. Chem., May 21, 2004; 279(21): 22243 - 22249. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Kienberger, R. Zhu, R. Moser, D. Blaas, and P. Hinterdorfer Monitoring RNA Release from Human Rhinovirus by Dynamic Force Microscopy J. Virol., April 1, 2004; 78(7): 3203 - 3209. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Henn, O. Medalia, S.-P. Shi, M. Steinberg, F. Franceschi, and I. Sagi Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy PNAS, April 5, 2001; (2001) 71372498. [Abstract] [Full Text]
|
|
|
|
 |
|
 C. Ma and R. J. Redfield Point Mutations in a Peptidoglycan Biosynthesis Gene Cause Competence Induction in Haemophilus influenzae J. Bacteriol., June 15, 2000; 182(12): 3323 - 3330. [Abstract] [Full Text]
|
|
|
|
 |
|
 L. J. Kricka Optical Tweezers and Immunoassay Clin. Chem., February 1, 1997; 43(2): 251 - 253. [Full Text] [PDF]
|
|
|
|
|
|
A. Henn, O. Medalia, S.-P. Shi, M. Steinberg, F. Franceschi, and I. Sagi Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy PNAS, April 24, 2001; 98(9): 5007 - 5012. [Abstract] [Full Text] [PDF]
|
|