RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis

Biomass production of site selective 13C/15N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR

Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large scale production of useful nucleotides. These nucleotides are site specifically labeled in C1′ and C5′ with minimal scrambling within the ribose ring. To demonstrate the utility of this labeling approach, the new site-specific labeled and the uniformly labeled nucleotides were used to synthesize a 36-nt RNA containing the catalytically essential domain 5 (D5) of the brown algae group II intron self-splicing ribozyme. The D5 RNA was used in binding and relaxation studies probed by NMR spectroscopy. Key nucleotides in the D5 RNA that are implicated in binding Mg2+ ions are well resolved. As a result, spectra obtained using selectively labeled nucleotides have higher signal-to-noise ratio compared to those obtained using uniformly labeled nucleotides. Thus, compared to the uniformly 13C/15N-labeled nucleotides, these specifically labeled nucleotides eliminate the extensive 13C–13C coupling within the nitrogenous base and ribose ring, give rise to less crowded and more resolved NMR spectra, and accurate relaxation rates without the need for constant-time or band-selective decoupled NMR experiments. These position selective labeled nucleotides should, therefore, find wide use in NMR analysis of biologically interesting RNA molecules

Design of photoactivated DNA oxidizing agents: synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines

A new series of photoactivated DNA oxidizing agents in which an acridine moiety is covalently linked to viologen by an alkylidene spacer was synthesized, and their photophysical properties and interactions with DNA, including DNA cleaving properties, were investigated. The fluorescence quantum yields of the viologen-linked acridines were found to be lower than that of the model compound 9-methylacridine (MA). The changes in free energy for the electron transfer reactions were found to be favorable, and the fluorescence quenching observed in these systems is explained by an electron transfer mechanism. Intramolecular electron transfer rate constants were calculated from the observed fluorescence quantum yields and singlet lifetime of MA and are in the range from 1.06×1010 s−1 for 1 a (n=1) to 6×108 s−1 for 1 c (n=11), that is, the rate decreases with increasing spacer length. Nanosecond laser flash photolysis of these systems in aqueous solutions showed no transient absorption, but in the presence of guanosine or calf thymus DNA, transient absorption due to the reduced viologen radical cation was observed. Studies on DNA binding demonstrated that the viologen-linked acridines bind effectively to DNA in both intercalative and electrostatic modes. Results of PM2 DNA cleavage studies indicate that, on photoexcitation, these molecules induce DNA damage that is sensitive to formamidopyrimidine DNA glycosylase. These viologen-linked acridines are quite stable in aqueous solutions and oxidize DNA efficiently and hence can be useful as photoactivated DNA-cleaving agents which function purely by the co-sensitization mechanism

One pot synthesis of acridinylalkanoic acids and novel bisacridines

The condensation reaction of diphenylamine with aliphatic dicarboxylic acids in presence of anhydrous zinc chloride gives rise to ω -(acridin-9-y1)alkan-α-oic acids and α ,ω-bis(acridin-9-yl)alkanes, in moderate to high yields, under defined experimental conditions

Steric and conformational effects on the photophysical and DNA binding properties of novel viologen linked tolylacridines

Two novel water soluble tolylacridines having viologen at the para and ortho to the acridine chromophore have been synthesized. Photophysical and DNA binding studies have revealed that the para-isomer exists in the extended conformation and binds to DNA by partial intercalation whereas the ortho-isomer exists both in folded and extended conformations and fails to interact with DNA

Structure of a self-splicing group II intron catalytic effector domain 5: Parallels with spliceosomal U6 RNA

Domain 5 (D5) is absolutely required for all catalytic functions of group II introns. Here we describe the solution NMR structure, electrostatic calculations, and detailed magnesium ion-binding surface of D5 RNA from the Pylaiella littoralis large ribosomal RNA intron (D5-PL). The overall structure consists of a hairpin capped by a GNRA tetraloop. The stem is divided into lower and upper helices of 8 and 5 bp, respectively, separated by an internal bulge. The D5-PL internal bulge nucleotides stack into the helical junction, resulting in a coupling between the bulge A25 and the closing base pair (G8–C27) of the lower helix. Comparison of the D5-PL structure to previously reported related structures indicates that our structure is most similar, in the helical regions, to the crystal structure of D5 from yeast Ai5γ (D5-Ai5γ) and the NMR structure of the U6 snRNA stem–loop region. Our structure differs in many respects from both the NMR and X-ray structures of D5-Ai5γ in the bulge region. Electrostatic calculations and NMR chemical shift perturbation analyses reveal magnesium ion-binding sites in the tetraloop, internal bulge, and the AGC triad in the lower stem. Our results suggest that the structure, electrostatic environment, and the magnesium ion-binding sites within the tetraloop, bulge, and triad regions are conserved features of the splicing machinery of both the group II introns and the spliceosome that are likely key for catalytic function

Halogenated squaraine dyes as potential photochemotherapeutic agents. Synthesis and study of photophysical properties and quantum efficiencies of singlet oxygen generation

We describe the synthesis and photophysical studies, including measurements of quantum yields of triplet excited states and singlet oxygen generation of bis(3,5-dibromo-2,4,6-trihydroxyphenyl)squaraine (2) and bis(3,5-diiodo-2,4,6-trihydroxyphenyl)squaraine (3). These dyes exist in solution in the protonated, neutral, single and double depro-tonated forms, depending on pH. The pK<SUB>a</SUB> values of these dyes were found to be relatively lower than those of the parent bis(2,4,6-trihydroxyphenyl)squaraine (1). Only the single deprotonated forms (Sq) of 2 and 3 showed measurable fluorescence. In microheterogeneous media such as in the presence of &#946;-cyclodextrin, cetyltrunethylammonium bromide and polyvinylpyrrolidone), bathochromic shifts in the absorption and emission spectra of Sq were observed with a substantial enhancement in their fluorescence yields. Triplet excited states are the main transient intermediates obtained upon 532 nm laser excitation of the various forms of 2 and 3 in methanol. These triplets have lifetimes in the range from 0.061 to 132 &#956;s. The triplet quantum yields of double deprotonated forms are low (&#966;<SUB>T</SUB> = &lt;0.01), whereas the neutral and Sq<SUP>-</SUP>forms of 2 (&#966;<SUB>r</SUB> = 0.12 and 0.22) and 3 (&#966;<SUB>T</SUB>= 0.24 and 0.5), respectively, exhibited significant triplet yields. Quantum yields of singlet oxygen generation by Sq<SUP>-</SUP>forms of 2 and 3 were determined in methanol and were found to be 0.13 and 0.47, respectively, which are in good agreement with the triplet yields obtained in these systems