pH-induced structural switch of a parallel duplex to triplex-DNA at a BOLF1 gene segment of the human herpes virus 4 (HH4) genome.

Conformational polymorphism exhibited by nucleic acids makes them potential tools in various fields of molecular biology, medicine, nanobiotechnology, and material science. The structural versatility associated with DNA and RNA forms the basis for developing oligonucleotide-based therapeutic strategies. Moreover, DNA's ability to respond to various physicochemical stimuli makes it a suitable candidate for biosensing applications. Naturally, two strands of the B-DNA duplex are oriented antiparallel to each other, stabilized by Watson-Crick hydrogen bonding. However, the formation of non-canonical DNA structures possessing varied base pairing schemes and strand orientation is also possible. Herein, a combination of UV-thermal denaturation, native polyacrylamide gel electrophoresis, and circular dichroism was used to investigate the structures formed by sequence-specific binding of a designed pyrimidine oligonucleotide to the target dodecamer (Pu.Py) segment of the BOLF1 gene of human herpesvirus 4 (HH4) genome. Through a curiosity-driven experiment, we report the formation of a parallel-stranded (ps) duplex at neutral pH, which transforms into a three-stranded DNA structure on lowering the pH. While the ps duplex is facilitated by reverse Watson-Crick; the triplex-DNA structure, formed at low pH, is stabilized by reverse Watson-Crick and Hoogsteen hydrogen bonding, resulting in an all-parallel-strand triple-stranded structure. To the best of our knowledge, any oligomeric structure consisting of all three strands (one Pu and two Py) in parallel orientation has not been characterized to date. Such a pH-mediated structural switching by DNA sequences may provide insights into the bioprocesses involving pH changes, both in vitro and in vivo, and towards the development of pH-based biosensors.