Potential G-quadruplexes and i-Motifs in the SARS-CoV-2

Abstract

Quadruplex structures have been identified in a plethora of organisms where they play important functions in the regulation of molecular processes, and hence have been proposed as therapeutic targets for many diseases. In this paper we report the extensive bioinformatic analysis of the SARS-CoV-2 genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for SARS-CoV-2. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, 512 potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over seventeen thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were then compared subsequently to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire viral realm. Sequences found in common with other viral species were further analyzed and characterized. Sequences with high scores unique to the SARS-CoV-2 were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates were then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable therapeutic targets for the SARS-CoV-2.

Differences in Vaccine and SARS-CoV-2 Replication Derived mRNA: Implications for Cell Biology and Future Disease

“…The changes to secondary structure can be observed in the G4 formations seen in each sequence using QGRSMapper (Figure 3) 5 . Similar trends were observed using G4-iM Grinder (Personal communication Belmonte) 12 . Does the increase of 4 to 19 G4 motifs alter the translation efficiency of these proteins?…”

“…Quadruplex G formations (G4s) in SARs-CoV-2 are highly conserved across over 16,466 SARs-CoV-2 genome sequences 9 . They are believed to play a critical role in transcription and translation of SARs-CoV-2 peptides [10][11][12] . G4 formations in the RNA sequence for nucleocapsid protein have been proposed as attractive drug targets to eliminate nucleocapsid expression.…”

G-Quadruplex Targeting in the Fight against Viruses: An Update

“…The urge of feasible therapies has boosted researchers worldwide to search for new strategies to fight the virus: one of these is the use of G4s as novel antiviral targets. Several bioinformatics tools were employed to assess the presence of PQSs within the SARS-CoV-2 RNA genome, showing very low enrichment in G4s [8,[99][100][101]. Nonetheless, the identified PQSs were shown to fold into two-layered G4s and to be located within the open reading frames (ORFs) 1ab and 3a, spike, membrane, and nucleocapsid genes, suggesting that RNA G4s could be involved in the regulation of viral replication, assembly, and immune-response modulation [99].…”

Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids

“…In eukaryotic cells, they occur in telomeres [8,9] and are over-represented in genomic promoter [10][11][12][13][14] and untranslated sequences [15][16][17], especially in genes and pathways involved in cancer initiation and progression [14,[18][19][20][21][22]. GQ-forming sequences have been found in the genomes of many organisms, ranging from viruses [23][24][25][26][27] to bacteria [28][29][30][31] and malaria [32][33][34]. GQs have been visualized in fixed [35][36][37][38] and in live cells [39][40][41][42], where their existence may be more than transient, with several roles in gene function [3,4,12]; for example, GQ folding is associated with sites of active transcription and precedes transcription itself [13,22].…”