Structure of the single-stranded polyribonucleotide polycytidylic acid

Arnott, Struther; Chandrasekaran, R.; Leslie, Andrew G. W.

doi:10.1016/0022-2836(76)90262-x

Cited by 104 publications

(68 citation statements)

References 37 publications

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“…Arnott et al studied poly(rC) fibers using x-ray diffraction, and proposed that the polynucleotide adopts a right-handed, six-fold helix with a rise between bases of 0.31 nm [39]. Broido and Kearns, however, found aspects of the x-ray structure of Arnott et al incompatible with their two-dimensional NMR results.…”

Section: Single-stranded C Tractsmentioning

confidence: 52%

Ultrafast excited-state dynamics of RNA and DNA C tracts

2008

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The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC) 18 were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC) 18 at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common basestacked structure, which may be identical with that of i-motif DNA.

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Section: Single-stranded C Tractsmentioning

confidence: 52%

Ultrafast excited-state dynamics of RNA and DNA C tracts

2008

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“…Interestingly, while we observe reactivity within the template, nucleotides 44-46 (CCC) consistently did not show reactivity above background levels, suggesting they may be stacked or involved in tertiary interactions. Polycytidylic acid alone can form a helix stabilized by base stacking or hydrogen bonding between adjacent bases (Arnott et al 1976;Freier et al 1981;Broido and Kearns 1982;Tubbs et al 2013). The CCC residues within the template could be adopting a similar structure, resulting in low NMIA reactivity.…”

Section: Resultsmentioning

confidence: 99%

Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE

Niederer

Zappulla

2014

RNA

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Telomerase catalyzes the addition of nucleotides to the ends of chromosomes to complete genomic DNA replication in eukaryotes and is implicated in multiple diseases, including most cancers. The core enzyme is composed of a reverse transcriptase and an RNA subunit, which provides the template for DNA synthesis. Despite extensive divergence at the sequence level, telomerase RNAs share several structural features within the catalytic core, suggesting a conserved enzyme mechanism. We have investigated the structure of the core of the human and yeast telomerase RNAs using SHAPE, which interrogates flexibility of each nucleotide. We present improved secondary-structure models, refined by addition of five base triples within the yeast pseudoknot and an alternate pairing within the human-specific element J2a.1 in the human pseudoknot, both of which have implications for thermodynamic stability. We also identified a potentially structured CCC region within the template that may facilitate substrate binding and enzyme mechanism. Overall, the SHAPE findings reveal multiple similarities between the Saccharomyces cerevisiae and Homo sapiens telomerase RNA cores.

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“…The distinct common feature of poly(rU), poly(dT), and poly(dC) is a lack of ordered local structure (Adler et al 1967;Evans and Sarma 1976;Cantor and Schimmel 1980). Despite the obvious similarities between poly(rC) and poly(dC) (except for the 2Ј-OH group present in poly(rC)), at neutral pH, unlike poly(dC), poly(rC) forms a narrow single-stranded helix that is stabilized by stacking interactions (Fasman et al 1964;Adler et al 1967;Arnott et al 1976;Garriga et al 1992). At neutral pH poly(rA) also forms single-stranded helical segments with a larger diameter than the poly(rC) helix that are interrupted by unstructured unstacked regions (Holcomb and Tinoco 1965;Saenger et al 1975).…”

Section: Discussionmentioning

confidence: 99%

Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association

Kolupaeva¹,

Unbehaun²,

Lomakin³

et al. 2005

RNA

115

131

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The multisubunit eukaryotic initiation factor (eIF) 3 plays various roles in translation initiation that all involve interaction with 40S ribosomal subunits. eIF3 can be purified in two forms: with or without the loosely associated eIF3j subunit (eIF3j+ and eIF3j−, respectively). Although unlike eIF3j+, eIF3j− does not bind 40S subunits stably enough to withstand sucrose density gradient centrifugation, we found that in addition to the known stabilization of the eIF3/40S subunit interaction by the eIF2·GTP·Met-tRNA i Met ternary complex, eIF3j−/40S subunit complexes were also stabilized by single-stranded RNA or DNA cofactors that were at least 25 nt long and could be flanked by stable hairpins. Of all homopolymers, oligo(rU), oligo(dT), and oligo(dC) stimulated the eIF3/40S subunit interaction, whereas oligo(rA), oligo(rG), oligo(rC), oligo(dA), and oligo(dG) did not. Oligo(U) or oligo(dT) sequences interspersed by other bases also promoted this interaction. The ability of oligonucleotides to stimulate eIF3/40S subunit association correlated with their ability to bind to the 40S subunit, most likely to its mRNA-binding cleft. Although eIF3j+ could bind directly to 40S subunits, neither eIF3j− nor eIF3j+ alone was able to dissociate 80S ribosomes or protect 40S and 60S subunits from reassociation. Significantly, the dissociation/anti-association activities of both forms of eIF3 became apparent in the presence of either eIF2-ternary complexes or any oligonucleotide cofactor that promoted eIF3/40S subunit interaction. Ribosomal dissociation and anti-association activities of eIF3 were strongly enhanced by eIF1. The potential biological role of stimulation of eIF3/40S subunit interaction by an RNA cofactor in the absence of eIF2-ternary complex is discussed.

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Structure of the single-stranded polyribonucleotide polycytidylic acid

Cited by 104 publications

References 37 publications

Ultrafast excited-state dynamics of RNA and DNA C tracts

Ultrafast excited-state dynamics of RNA and DNA C tracts

Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE

Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association

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