A novel DNA duplex. A parallel-stranded DNA helix with Hoogsteen base pairing

Abstract

We show here for the first time that a stable parallel double helix with Hoogsteen pairing can exist independently of the triple helix of which it is a component part. The experiments employ DNA oligonucleotides with mixed sequences of normal bases. These duplexes are distinct from previously reported ribopolynucleotide helices containing bulky substituents which prevent Watson-Crick pairing as well as from parallel duplexes with Donohue, or reversed Watson-Crick, pairing. Stoichiometry is established by mixing curves and gel electrophoresis. Tm depends linearly upon pH, increasing with acidity because of the need to protonate N3 of C. The Tm of the 20-mer studied here is 52 degrees C at pH 5.2 and 0.1 M NaCl. At pH above 6, the molecule rearranges to form an antiparallel duplex with imperfect Watson-Crick pairing and loops, and the Tm is then independent of pH. The CD spectrum of the parallel duplex is very similar to that of the corresponding triple helix but quite different from that of the Watson-Crick helix. The infrared spectrum 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 form 800 to 1000 cm-1, which is sensitive to backbone conformation. The only symmetry element present is a pseudorotational axis coincident with the helix axis of the parallel duplex as well as with the axis of the corresponding triple helix.(ABSTRACT TRUNCATED AT 250 WORDS)

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

“…The duplex is clearly antiparallel, as is apparent from the electron density distribution along the phosphodiester polymer chains; thus, it is not related to parallel DNA, which differs in the relative orientation of the phosphodiester chains. Parallel DNA may show different hydrogen bonding schemes, either reverse Watson-Crick (28) or Hoogsteen (29), as found in our structure. However, parallel DNA appears to be only marginally stable and rearranges easily into conventional structures (30).…”

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

“…Instead, the system prefers to accommodate mismatches either in antiparallel duplex (neutral pH) or triplex with a free purine strand (acidic pH). This shows the comparative lower stability of parallel duplexes, proposed by Liu et al (31) and Raghunathan et al (32).…”

Homopurine and homopyrimidine strands complementary in parallel orientation form an antiparallel duplex at neutral pH with A-C, G-T, and T-C mismatched base pairs

“…1,2,32,33 In mildly acidic conditions, cytosine N3 is protonated and Hoogsteen A-T and G-C / base pairs can stabilize a parallel While Watson-Crick (WC) is the normal hydrogen-bonding scheme in complementary DNA du-DNA duplex. Parallel-stranded purine-pyrimidine stretches also form part of triplexes, tetraplexes, and plexes 1-3 mismatch base pairs are often formed during replication and genetic recombination.…”