Guanine rich sequences in genome of SARS-CoV-2

Z gvanini bogata zaporedja s tipično obliko GnXaGnXbGnXcGn, kjer so Gn neprekinjeni gvaninski traktin ≥ 27 ≥ a/b/c ≥ 0X pa je poljubni nukleotid, so zmožna tvorbe G-kvadrupleksnih struktur. Pogosta so v regulatornih regijah virusnih genomov, vendar so v genomu SARS-CoV-2 redka. Ligandi za virusne G-kvadruplekse imajo velik terapevtski potencial. Netipične G-kvadrupleksne strukture lahko vsebujejo izbokline in lasnične zanke, ki hkrati predstavljajo dodatna vezavna mesta za ligande. Netipična G-kvadrupleksna zaporedja smo iskali v genomu SARS-CoV-2, za kar smo na podlagi G4Hunter algoritma napisali posodobljeni algoritem imenovan G4HunterHairpin. To je prvi znan algoritem, ki v iskanju zaporedij, zmnožnih tvorbe G-kvadrupleksov, vključuje iskanje lasnic v prekinjenih G-traktih. Z G4HunterHairpin smo v genomu SARS-CoV-2 našli oligonukleotidna zaporedja z napovedanim zvitjem v netipične G-kvadrupleksne strukture. Sintetizirali smo 13 oligonukleotidov ter jih analizirali z 1D 1H NMR spektroskopijo. Opazili smo tvorbo lasnic ali G-kvadrupleksov, pri čemer smo pri oligonukleotidu V8-30 opazili tvorbo obeh struktur hkrati. Z 2D 1H-1H NOESY eksperimentom smo določili paralelno topologijo V8-30 G-kvadrupleksa ter asignirali nekatere bazne pare v lasnici.Guanine-rich sequences with a typical form of GnXaGnXbGnXcGn, where Gn are guanine tractsn ≥ 27 ≥ a/b/c ≥ 0 and X is any nucleotide, are capable of forming G-quadruplex structures. They are common in the regulatory regions of viral genomes, but rare in the SARS-CoV-2 genome. Ligands for viral G-quadruplexes have great therapeutic potential. Atypical G-quadruplex structures can contain bulges and hairpin loops which may represent additional binding sites for ligands. Atypical G-quadruplex forming sequences were searched for in the SARS-CoV-2 genome, for which we wrote an updated algorithm based on the G4Hunter algorithm named G4HunterHairpin. This is the first known algorithm to include the search for hairpins in interrupted G-tracts. Using G4HunterHairpin, we found oligonucleotide sequences in the SARS-CoV-2 genome with predicted folding into atypical G-quadruplex structures. We synthesised 13 oligonuclotides and analysed them using 1D 1H NMR spectroscopy. The formation of hairpins or G-quadruplexes was observed, with simultaneous formation of both structures observed for oligonucleotide V8-30. The latter was further characterised by 2D 1H-1H NOESY spectroscopy, from which the parallel topology of the G-quadruplex was determined and certain base pairs in the hairpin were assigned