APPENDIX B - Letter for fifth discussion

Charles Yanofsky writes, “I have been reading a recent article by J. Widom in the November 22 PNAS issue on target site location by DNA binding proteins. It appears that DNA binding sites can exist in two states and that this determines their ability to be recognized by proteins. Another variable for nature to exploit!

Henry Sobell replies “Sounds interesting! I will look into this!”

[Charles Yanofsky is a Professor of Biology at Stanford University, having led the way in understanding how the multigenic tryp operon is regulated in Escherichia coli].

In addition to premeltons, are there other kinds of “discrete breathers” in DNA?

Yes – at higher energies -- two additional types of ‘discrete breathers’ exist. The first, “branch migratons”, arise at base sequences containing 2-fold symmetry, while the second, “dislocatons”, arise at base sequences containing iterative dinucleotide base sequences. Both originate within the centers of premeltons. The presence of branch migratons and paired dislocatons can be detected through the use of the S1 nuclease – an enzyme that recognizes single-stranded DNA regions present within these structures. Sensitivity to S1 cleavage is a convenient way to monitor their appearance, and this provides yet another example of how a nuclease detects alterations in DNA structure due to the presence of a discrete breather in DNA.

What about the B- (or A-) to Z- transition -- a structural phase transition that occurs in DNA?

How does the presence of ethidium “reverse” this transition?

[NOTE: Z-DNA is a left-handed DNA conformation that forms within certain types of alternating purine-pyrimidine sequences, notably alternating guanine-cytosine (it also occurs in RNA). Z-DNA was first detected by X-ray crystallography in Alexander Rich’s lab at MIT, and then subsequently verified to exist in long chain DNA by other investigators working in the molecular biology area].

Finally, --how do premeltons arise in B- (or A-) DNA, and, once formed, go on to nucleate DNA melting?

What is the mechanism of DNA melting?

It is interesting to note that DNA melting and the formation of branch migratons and dislocatons are related phenomena. DNA melting is a thermally driven process, energies coming from the fluctuations. The formation of branch migratons and dislocations -- and their ability to undergo branch migration – on the other hand, not only reflects energies coming from the fluctuations, but also from torsional strain energies present in negatively superhelical DNA molecules. The latter arises from the conversion of the left-handed toroidal superhelical form to the right-handed interwound superhelical form.

Henry Sobell

Alwyn Scott