Structural Insights into Human Adenovirus Type 4 Virus-Associated RNA I.

Helen Bergquist,Tanel Punga,Raviteja Inturi,Rula Zain

doi:10.3390/ijms23063103

Abstract

RNA molecules can adopt specific RNA triplex structures to execute critical biological functions. Human adenoviruses (HAdVs) are abundant pathogens encoding the essential, noncoding virus-associated RNA I (VA RNAI). Here, we employ a triplex-specific probing assay, based on the intercalating and cleaving agent benzoquinoquinoxaline 1, 10-phenanthroline (BQQ–OP), to unravel a potential RNA triplex formation in VA RNAI. The BQQ–OP cleavage of the pathogenic HAdV type 4 (HAdV-4) VA RNAI indicates that a potential triplex is formed involving the highly conserved stem 4 of the central domain and side stem 7. Further, the integrity of the HAdV-4 VA RNAI side stem 7 contributes to a potential triplex formation in vitro and virus growth in vivo. Collectively, we propose that the HAdV-4 VA RNAI can potentially form a biologically relevant triplex structure.

Highlights

We demonstrated that BQQ–OP cleaves the Human adenoviruses (HAdVs)-4 virus-associated RNA I (VA RNAI) at the conserved 50 -GGGU30 motif and that this particular cleavage is influenced by the sequence integrity at the conserved stem 4 of the central domain and protruding stem 7
We have previously shown that different VA RNAI molecules originating from the
Our results indicate that the BQQ–OP causes specific VA RNAI cleavage, which could be due to the possible formation of an intramolecular triplex structure within the VA RNAI molecule

Summary

Introduction

In order to carry out these critical functions, the RNA molecules often adopt specific three-dimensional structures. The three-dimensional structure is promoted by the maximization of base stacking, electrostatic stabilizations, and hydrophobic interactions [2]. The tertiary structure is stabilized through the formation of different types of hydrogen bonds, including minor groove interactions, Watson–Crick, Hoogsteen, and reverse Hoogsteen base-pairing leading to tetraloops and triple-strand structures [3]. The triplex structures form when a third, single-stranded nucleotide chain binds in a sequencespecific manner to a polypurine/polypyrimidine duplex. The nucleobases of the third strand can either be purines or pyrimidines, and they bind to the polypurine stretch of the duplex via Hoogsteen or reverse Hoogsteen hydrogen bonds [4]. The stability of a given triplex structure is dependent on the sequence and on the surrounding environment, including the salt concentration, pH, and triplex-interacting proteins [5,6]

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