Abstract: Parallel DNA helices with reverse Watson-Crick pairing have been described in several papers. It has been pointed out, however, that the parallel structures may also be in equilibrium with antiparallel Watson-Crick helices due to their closely similar properties. To avoid the problem we have prepared, characterized DNA helices which are constrained to possess parallel polarity by two dC residues, or "CC⁺ clamps", at both the ends of AT oligomer chains. The residues are hemiprotonated below neutral pH, forming two stable CC⁺ base pairs with three hydrogen bonds at each end of the helix. The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues. Though recent studies indicate that dC acid self-structures are four-stranded with intercalated bases, gel electrophoresis indicates that these structures are not present in the molecules described here.

Key words: Parallel DNA helices, Reverse Watson-Crick pairing, CC⁺base pair, Oligonucleotide