Comparative studies on the secondary structure of eukaryotic 5.8S ribosomal RNA

Van, Nguyen T.; Nazar, Ross N.; Sitz, Thomas O.

doi:10.1021/bi00636a004

Cited by 31 publications

(19 citation statements)

References 9 publications

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“…The changes in absorbance at various wavelengths for this curve match those obtained elsewhere for melting of an RNA of over 90% G + C, as indicated in the figure (6). The change in absorbance at 260 nm is 18% which also indicates over 90% G + C content, (6,19). Difference spectra were calculated for the early (160 to 780C) and the late (780 to 910C) parts of the melting process.…”

Section: Resultssupporting

confidence: 81%

“…A-U pairs (6,15,19). Given the size and sequence of the fragment, this means that only one A-U pair could exist per mole of monomer and this situation disallows the dimer form which would contain two moles of A-U pairs per mole of monomer, i.e., 20% A-U.…”

Section: Discussionmentioning

confidence: 99%

“…Predicted secondary structures for mammalian and yeast 5.8S rRNAs agree on the existence of a common G + C rich hairpin helix of 9 base pairs (2,7). This hairpin is demonstrable in melting studies of the whole molecule (6) and appears to be part of a nearly 30 base pair dimeric helix in the 5.8S -28S rRNA junction complex (8),…”

Section: Introductionmentioning

confidence: 98%

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Thermodynamics of a stable yeast 5.8S rRNA hairpin helix

Lightfoot¹

1978

Nucl Acids Res

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The 5. 8S ribosomal RNA of bakers yeast contains one particularly stable hairpin helix which is isolated by partial T1 ribonuclease digestion. Thermal hyperchromism analysis of the hairpin fragment showed that it dissociates cooperatively with 18% hyperchromism, with a Tm of 83 degree C at 2.7 mM sodium ion concentration, and with a hyperchromic difference spectrum indicative of over 90% G + C content. The probable secondary structure for the fragment was used to predict a helix free energy, delta G = -16.2 kcal/mole, which was the same as that determined from the melting equilibrium. The predicted enthalpy however, was 77% of the value, delta H = -114 kcal/mole, determined from the van't Hoff relationship. The effect on these data of a G.U base pair within the 9 base pair helix is discussed.

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Section: Resultssupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

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Thermodynamics of a stable yeast 5.8S rRNA hairpin helix

Lightfoot¹

1978

Nucl Acids Res

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“…Based on ethidium bromide binding, Van et al. (24) reported that yeast 5.8S RNA contains about twice as many U-A base pairs as does Novikoff hepatoma 5.8S RNA, in agreement (Table 2) with the cloverleaf (23 pairs vs. 12 pairs). Those authors also predicted a G-C/A-U ratio close to 1 for yeast 5.8S RNA, and a stable stem region and similar degree of base pairing for both yeast and rat 5.8S RNA, again consistent with the cloverleaf structure.…”

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confidence: 66%

Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA.

Luoma¹,

Marshall²

1978

Proc. Natl. Acad. Sci. U.S.A.

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Neither of the two previously proposed secondary structures for eukaryotic 5.8S RNA is consistent with the present laser Raman results. A new, highly stable "cloverleaf" secondary structure not only fits the Raman data but also accounts for previously determined enzymatic partial cleavage patterns, base sequence and pairing homologies, and GC and A'U base pair numbers and ratios. The new cloverleaf model also conserves several structural features (constant loops, bulges, and stems) consistent with known 5.8S RNA functions. Finally, we propose a similar new cloverleaf secondary structure for Escherichia coli 5S RNA, consonant with many known properties of prokaryotic 5S RNA. 5S RNA and 5.8S RNA belong to a class of small RNA molecules (including tRNA) that function in protein synthesis. The structure and function of the smaller tRNA is now understood largely because (i) tRNAPhe has been successfully crystallized and its three-dimensional structure has been determined (1, 2), and (ii) tRNA function is present in part in the free cytoplasm. In contrast, 5S RNA and 5.8S RNA are intimately bound to the ribosome. Their three-dimensional crystal structures have not yet been reported, and conclusions based on low-field hydrogen-bonded proton nuclear magnetic resonance spectra have been severely limited by poor resolution (3, 4). Less-direct structural information from other techniques has been reviewed (5), and more recent results are now discussed.Pene et al. (6) demonstrated that 5.8S RNA is strongly hydrogen-bonded to the 28S RNA of the large ribosomal subunit of eukaryotes. This interaction is between the 3' end of the 5.8S RNA molecule and a complementary segment of the 288 RNA and is stabilized by the presence of a G-C-rich loop near the 3' end of the 5.8S RNA (7). Moreover, all 5.8S RNA nucleotide sequences determined to date contain a sequence of bases that is complementary to the T4/CG-loop of tRNA (8-10). These facts suggest that 5.8S RNA in eukaryotes binds tRNA at the ribosome during transcription.In addition, the following facts connect the structure and function of eukaryotic 5.8S RNA to prokaryotic 5S RNA. First, yeast 5.8S RNA can bind the same ribosomal proteins (EL-18 and EL-25) that Escherichia coli 5S RNA binds most strongly, and this 5.8S RNA-E. colh protein complex exhibits GTPase and ATPase activities similar to those for the homologous 5S RNA-protein complex (11). Second, all prokaryotic 5S RNA molecules contain the complement of the TXCG-loop of tRNA and can bind the tetranucleotide UUCG (5). Third, both the prokaryotic 5S RNA sequence and the eukaryotic 5.8S RNA sequence are contained in the large ribosomal RNA transcription units (12). Therefore, because eukaryotic 5.8S RNA and prokaryotic 5S RNA appear to have similar origin and function, their secondary structures should be similar.Raman spectroscopy has proved to be a sensitive probe ofThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in a...

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“…The spectral dependence of the melting hyperchromism may be used to characterize the denaturation of nucleic acids secondary structures (31)(32)(33). Indeed, G-C and A-U base pairs show very distinct denaturation spectra.…”

Section: Spectral Dependence Of the Relaxation Amplitudesmentioning

confidence: 99%

Temperature Jump Relaxation Studies on the Interactions Between Transfer RNAs with Complementary Anticodons. The Effect of Modified Bases Adjacent to the Anticodon Triplet

Houssier¹,

Grosjean²

1985

Journal of Biomolecular Structure and Dynamics

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We have used the temperature-jump relaxation technique to determine the kinetic and thermodynamic parameters for the association between the following tRNAs pairs having complementary anticodons: tRNA(Ser) with tRNA(Gly), tRNA(Cys) with tRNA(Ala) and tRNA(Trp) with tRNA(Pro). The anticodon sequence of E. coli tRNA(Ser), GGA, is complementary to the U*CC anticodon of E. coli tRNA(Gly(2] (where U* is a still unknown modified uridine base) and A37 is not modified in none of these two tRNAs. E. coli tRNA(Ala) has a VGC anticodon (V is 5-oxyacetic acid uridine) while tRNA(Cys) has the complementary GCA anticodon with a modified adenine on the 3' side, namely 2-methylthio N6-isopentenyl adenine (mS2i6A37) in E. Coli tRNA(Cys) and N6-isopentenyl adenine (i6A37) in yeast tRNA(Cys). The brewer yeast tRNA(Trp) (anticodon CmCA) differs from the wild type E. coli tRNA(Trp) (anticodon CCA) in several positions of the nucleotide sequence. Nevertheless, in the anticodon loop, only two interesting differences are present: A37 is not modified while C34 at the first anticodon position is modified into a ribose 2'-O methyl derivative (Cm). The corresponding complementary tRNA is E.coli tRNA(Pro) with the VGG anticodon. Our results indicate a dominant effect of the nature and sequence of the anticodon bases and their nearest neighbor in the anticodon loop (particularly at position 37 on the 3' side); no detectable influence of modifications in the other tRNA stems has been detected. We found a strong stabilizing effect of the methylthio group on i6A37 as compared to isopentenyl modification of the same residue. We have not been able so far to assess the effect of isopentenyl modification alone in comparison to unmodified A37. The results obtained with the complex yeast tRNA(Trp)-E.coli tRNA(Pro) also suggest that a modification of C34 to Cm34 does not significantly increase the stability of tRNA(Trp) association with its complementary anticodon in tRNA(Pro). The observations are discussed in the light of inter- and intra-strand stacking interactions among the anticodon triplets and with the purine base adjacent to them, and of possible biological implications.

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Comparative studies on the secondary structure of eukaryotic 5.8S ribosomal RNA

Cited by 31 publications

References 9 publications

Thermodynamics of a stable yeast 5.8S rRNA hairpin helix

Thermodynamics of a stable yeast 5.8S rRNA hairpin helix

Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA.

Temperature Jump Relaxation Studies on the Interactions Between Transfer RNAs with Complementary Anticodons. The Effect of Modified Bases Adjacent to the Anticodon Triplet

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