Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA

Tuning the Computational Evaluation of Spectroscopic, ELF, LOL, NCI analysis and Molecular Docking of Novel Anti COVID-19 Molecule 4-Dimethylamino Pyridinium 3, 5-Dichlorosalicylate

In this work novel antiviral compound 4-(Dimethylamino) Pyridinium 3, 5-dichlorosalicylate was synthesized and characterized by UV-vis, FT-IR, FT-Raman, 1H NMR and 13C NMR spectra. Quantum chemical computations were carried out by Density functional theory methods at B3LYP level. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization is investigated using natural bond orbital analysis. Assignments of vibrational spectra have been carried out with the aid of Normal coordinate analysis following the SQMFF methodology. TD-DFT approach was applied to assign the electronic transition observed in UV visible spectrum measured experimentally. Frontier molecular orbital energy gap affirms the bioactivity of the molecule and NCI analysis gives information about inter and intra non covalent interactions. ESP recognises the nucleophilic and electrophilic regions of molecule and the chemical implication of molecule was explained using ELF, LOL. The reactive sites of the compound were studied from the Fukui function calculations and chemical descriptors define the reactivity of the molecule. Molecular docking done with SARS and MERS proteins endorses the bioactivity of molecule and drug likeness factors were calculated to comprehend the biological assets of DADS.

Selective Enzymatic Demethylation of N2 ,N2 -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing

The abundant Watson-Crick face methylations in biological RNAs such as N¹ -methyladenosine (m¹ A), N¹ -methylguanosine (m¹ G), N³ -methylcytosine (m³ C), and N² ,N² -dimethylguanosine (m²₂ G) cause significant obstacles for high-throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild-type E. coli AlkB and its D135S mutant can remove most of m¹ A, m¹ G, m³ C modifications in transfer RNA (tRNA), but they work poorly on m²₂ G. Here we report the design and evaluation of a series of AlkB mutants against m²₂ G-containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m²₂ G modification to N² -methylguanosine (m² G). We also show that this new enzyme improves the efficiency of tRNA sequencing.

Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions

Post-transcriptional modifications play important roles in modulating the functions of RNA species. The presence of modifications in RNA may directly alter its interactions with binding partners or cause structural changes that indirectly affect ligand recognition. Given the rapidly growing list of modifications identified in noncoding and mRNAs associated with human disease, as well as the dynamic control over modifications involved in various physiological processes, it is imperative to understand RNA structural modulation by these modifications. Among the RNA species, rRNAs provide numerous examples of modification types located in differing sequence and structural contexts. In addition, the modified rRNA motifs participate in a wide variety of ligand interactions, including those with RNA, protein, and small molecules. In fact, several classes of antibiotics exert their effects on protein synthesis by binding to functionally important and highly modified regions of the rRNAs. These RNA regions often display conservation in sequence, secondary structure, tertiary interactions, and modifications, trademarks of ideal drug-targeting sites. Furthermore, ligand interactions with such regions often favor certain modification-induced conformational states of the RNA. Our laboratory has employed a combination of biophysical methods such as nuclear magnetic resonance spectroscopy (NMR), circular dichroism, and UV melting to study rRNA modifications in functionally important motifs, including helix 31 (h31) and helix h44 (h44) of the small subunit rRNA and helix 69 (H69) of the large subunit rRNA. The modified RNA oligonucleotides used in these studies were generated by solid-phase synthesis with a variety of phosphoramidite chemistries. The natural modifications were shown to impact thermal stability, dynamic behavior, and tertiary structures of the RNAs, with additive or cooperative effects occurring with multiple, clustered modifications. Taking advantage of the structural diversity offered by specific modifications in the chosen rRNA motifs, phage display was used to select peptides that bind with moderate (low micromolar) affinity and selectivity to modified h31, h44, and H69. Interactions between peptide ligands and RNAs were monitored by biophysical methods, including electrospray ionization mass spectrometry (ESI-MS), NMR, and surface plasmon resonance (SPR). The peptides compare well with natural compounds such as aminoglycosides in their binding affinities to the modified rRNA constructs. Some candidates were shown to exhibit specificity toward different modification states of the rRNA motifs. The selected peptides may be further optimized for improved RNA targeting or used in screening assays for new drug candidates. In this Account, we hope to stimulate interest in bioorganic and biophysical approaches, which may be used to deepen our understanding of other functionally important, naturally modified RNAs beyond the rRNAs.

Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.