Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Are Micrococcal Nuclease Hypersensitive Sites the Centers of PREMELTONS Present in Naked DNA Molecules?

The above study demonstrates the remarkable similarities between the intercalator, 1,10-phenanthroline copper (I), and the micrococcal nuclease in their ability to recognize and to cleave hypersensitive sites in a naked 5,000 base pair circular DNA fragment containing the histone gene cluster from D. melanogaster (1).

Circularized naked DNA molecules, previously labeled with radioactive phosphorous at a single Bam H1 site, were first incubated with either the micrococcal nuclease or 1, 10-phenanthroline copper (I), and the reaction followed as a function of time.

The resulting fragments were then cleaved with Hind III to give fragments having a common Hind III end, this being 68 base pairs downstream from the labeled Bam site. Slab gel electrophoresis in 1% agarose, followed by autoradiography, was then used to visualize radioactively labeled fragments containing different DNA chain lengths.

As shown, the cleavage patterns exhibited by both agents are amazingly similar. Hypersensitive sites are seen to be primarily at the 5' ends of genes, and also to lie between adjacent genes.

What is even more remarkable is the observation that many of these sites nucleate melting when the single-strand specific DNA binding protein of E. coli is added in the presence of negative superhelicity in DNA. The location of these small melted DNA regions has been established using S1 nuclease, in combination with electron microscopy (2).

What is the nature of these micrococcal nuclease hypersensitive sites, and how are they related to the onset of DNA melting?

Earlier, I proposed micrococcal nuclease hypersensitive sites to be the centers of premeltons ?- these being examples of ?discrete breathers? in DNA (3?5). More generally, discrete breathers are breather solitons (these are also known as kink-antikink bound states). They have their own identity, undergoing unique nonlinear dynamical motions called breather motions. Discrete breathers have been studied extensively over the years by both physicists and mathematicians working in different areas of nonlinear science (6, 7).

I will review the evidence that supports my proposal through the use of a website specially created for this purpose. This will be shown on a lap top computer available at the time of the meeting.

References and Footnotes
  1. Jessee, G., Gargiulo, G., Razvi, F., and A. Worcel. Nucleic Acids Research 10, 5823-5834 (1982).
  2. G. C. Glickin, G. Gargiulo, L. Rena-Descalzi, and A. Worcel. Nature 303, 770-774 (1983).
  3. A. Banerjee and H. M. Sobell. Journal of Biomolecular Structure and Dynamics 1, 253-262 (1983).
  4. H. M. Sobell. Proc. Nat. Acad. Sci. USA 82, 5328-5331 (1985).
  5. H. M. Sobell, Kink-Antikink Bound States in DNA Structure in Biological Macromolecules and Assemblies, Volume 2, Nucleic Acids and Interactive Proteins, pp. 172-232. Eds., F. A. Jurnack and A. McPherson. John Wiley & Sons, New York (1985).
  6. Nonlinear Science, Second Edition. Alwyn Scott, Oxford University Press (2003).
  7. Encyclopedia of Nonlinear Science. Ed., Alwyn Scott, Routledge, Taylor and Francis Group (2005).

Henry M. Sobell

Lake Luzerne, NY 12846

Email: sobell@localnet.com