AFM of single-stranded RNA, triple-stranded DNA and helix turns

Single-stranded RNA

Single-stranded polyA (A, B) differs from double-stranded DNA mainly in its persistence length. The persistence length of ss polyA is ca. 40 nm, while the persistence length of dsDNA under the same conditions is ca. 80 nm. PolyA in water also protonates to form a very stiff double helix with a persistence length of ca. 600 nm, (e.g., arrow in B) Images are 1 mm2. (From (1).)

Triple-stranded DNA

Features that appear to be triple-stranded DNA can be seen on poly(dA):poly(dT) (A, B) and poly(dG):poly(dC). The putative triple-stranded DNA is ca. twice as high as dsDNA. Images are 1 mm2. (From (1).)

Helix turns on dsDNA (2)

The best images of helix turns with tapping AFM show more detail than images of helix turns with contact AFM (3, 4). These helix turns were imaged in propanol with an unusually good tip and cannot be obtained reliably. Scale bar is 10 nm. Shao's group can see helix turns on dsDNA much more reproducibly but in less detail than the above image, using samples of densely packed DNA on a positively charged lipid bilayer, imaged with contact AFM (3). We have not yet been able to image such a sample with tapping AFM to see if the helix turns can be resolved in more detail. The DNA in propanol shows intriguing deformations of the double helix where the DNA bends sharply that would be fascinating to image more. We believe that only the major groove was detected, because the periodicities are 3-4 nm. Densely packed DNA on lipid should be better for getting high resolution, because there is less interaction between the tip and the DNA than with isolated DNA molecules (5).


1. Hansma, H. G., I. Revenko, K. Kim, and D. E. Laney. 1996. Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res. 24:713-720.

2. Hansma, H. G., M. Bezanilla, D. L. Laney, R. L. Sinsheimer, and P. K. Hansma. 1995. Applications for Atomic Force Microscopy of DNA. Biophys. J. 68:1672-1677.

3. Mou, J., D. M. Czajkowsky, Y. Zhang, and Z. Shao. 1995. High-resolution atomic-force microscopy of DNA: the pitch of the double helix. FEBS Lett. 371:279-282.

4. Hansma, H. G., and P. K. Hansma. 1993. Potential applications of atomic force microscopy of DNA to the human genome project. Proc. SPIE - Int. Soc. Opt. Eng. (USA). 1891:66-70.

5. Hansma, H. G. 1995. Polysaccharide helices in the atomic force microscope. Biophys. J. 68:3-4.