Re: What are the base pairing rules for triplex DNA?

A recent collaborative work on the subject DNA triplexes coming out of Lake Forest College, the University of Barcelona, and the University of Nottingham can be accessed online at http://chem3.lfc.edu/research/MGMS/. This site covers most of the salient points of triplex DNA, along with a very indepth look at its Molecular Modeling, so I won't try to explain it here. To answer your questions point by point: The third strand runs parallel to the minus strand, with which it base-pairs through Hoogsteen hydrogen bonding; the nature of these bonds require a stretch of purines (A or G) along the minus strand, such that all of the known DNA triplexes have been poly-d(C): poly- d(G): poly-d(C) or more recently poly-d(T): poly-d(A): poly-d(T); and finally, environmental changes in pH or salt concentration, or mechanical changes in supercoiling (possibly via an intercalating agent) can quickly destabilize the DNA triplex. Again, a much more thorough discussion is available at the above website, so go there if you have more questions, or check any Nucleic Acids textbook - "Genes VI" by Benjamin Lewin is the favorite in the Molecular Genetics community.