A NOVEL DNA DUPLEX - A PARALLEL-STRANDED DNA HELIX WITH HOOGSTEEN BASE-PAIRING

We show here for the first time that a stable parallel double helix wi th Hoogsteen pairing can exist independently of the triple helix of wh ich it is a component part. The experiments employ DNA oligonucleotide s with mixed sequences of normal bases. These duplexes are distinct fr om previously reported ribopolynucleotide helices containing bulky sub stituents which prevent Watson-Crick pairing as well as from parallel duplexes with Dronohue, or reversed Watson-Crick, pairing. Stoichiomet ry is established by mixing curves and gel electrophoresis. T(m) depen ds linearly upon pH, increasing with acidity because of the need to pr otonate N3 of C. The T(m) of the 20-mer studied here is 52-degrees-C a t pH 5.2 and 0.1 M NaCl. At pH above 6, the molecule rearranges to for m an antiparallel duplex with imperfect Watson-Crick pairing and loops , and the T(m) is then independent of pH. The CD spectrum of the paral lel duplex is very similar to that of the corresponding triple helix b ut quite different from that of the Watson-Crick helix. The infrared s pectrum in the double bond region closely resembles that of the triple helix but, as with the CD, is quite different from that of the Watson -Crick duplex. The infrared spectra of the duplex and triple helix are also nearly identical in the region from 800 to 1000 cm-1, which is s ensitive to backbone conformation. The only symmetry element present i s a pseudorotational axis coincident with the helix axis of the parall el duplex as well as with the axis of the corresponding triple helix. We suggest that structural and spectroscopic properties of the triple helix are determined by the Hoogsteen-paired strands and not by the Wa tson-Crick-paired component strands.