page_title: Polypurine reverse-Hoogsteen hairpin
section_title: Design and improvements
hierarchical_section_title: Polypurine reverse-Hoogsteen hairpin / Design and improvements
caption_attribution_description: English: Change of nucleotide in the PPRH when targeting a polypurine stretch with purine interruptions.
context_page_description: Polypurine reverse-Hoogsteen hairpins are non-modified oligonucleotides containing two polypurine domains, in a mirror repeat fashion, linked by a pentathymidine stretch forming double-stranded DNA stem-loop molecules. The two polypurine domains interact by intramolecular reverse-Hoogsteen bonds allowing the formation of this specific hairpin structure.
context_section_description: PPRHs can be designed for virtually any gene in the genome by searching for polypirimidine stretches in the sequence of the desired gene. Optimal lengths for each domain of the PPRHs are within 20–30 nucleotides. The total length of a typical PPRH is 55 nucleotides considering two domains of 25 bases plus 5T for the linking loop. If purine interruptions are encountered (up to three) within the polypirimidine target, the highest affinity of PPRH binding is achieved by placing in the hairpin the complementary base (a pyrimidine) in front of the purines (Wild type-PPRH).
caption: Wild type-PPRH: Version of PPRH containing a pyrimidine in front of purine interruptions in the DNA target.
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