Conformational Analysis of the Nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from Nuclear Magnetic Resonance and Circular Dichroism Studies

Doornbos, Johannes; Hartog, J.; Boom, Jacques H. van; Altona, C.

doi:10.1111/j.1432-1033.1981.tb05349.x

Cited by 51 publications

(20 citation statements)

References 37 publications

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“…With the aid of a 20-J-resolved spectrum of 3, as depicted in Figure 7, and the T 1 sub-spectra for the triribonucleotides (see Figures 3IB and 3IIB), the coupling constants J 1 • 2 • and J 3 • 4 • are obtained (Table II), and the percentSconformation for each residue ofthe three compounds are calculated. The results of the population analysis, as tabulated in Table III, indicate that the trimers exist as a mixture of S-and N-conformers, and with a slight preference for the latter form which is in accord with a previously examined 2' -5' linked dinucleotide (52). In all the three cases, the stacking modes are s;·.~ with the central adenine moiety having the highest S-population.…”

Section: Conformation Of the Ribose Rings And Handedness Of The Brancsupporting

confidence: 59%

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR

Huss

Gosselin

et al. 1987

Journal of Biomolecular Structure and Dynamics

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The non-exchangeable 1H-NMR signals of the branch core trinucleotide of the lariat branch site (A2'p5'G3'p5'C, 1) and its derivatives 2 and 3 are completely assigned using one- and two-dimensional NMR techniques including NOE, COSY, NOESY, 1H-1H INADEQUATE and 2D-J-resolved spectroscopy. From the vicinal coupling constants in the individual ribose rings, NOE data and T1 measurements, the following properties of the trimers are deduced. (i) The unique stacking behavior of the trimers is S2'N3'N, and the sugar rings exist predominantly in the N-conformation (3'-endo-2'-exo). (ii) The sugar-base orientations appear to be anti. (iii) The branched trimers exist in solution as single-stranded right-handed conformations resembling A-RNA with stacking between the adenine and guanine residues in aqueous solution at 21 degrees C and pH 7.2. (iv) The calculated values for the torsion angles epsilon t and gamma+ for the trimers are 201-203 degrees and 71-86%, respectively, while the percent beta t values are higher for the guanine (87-92%) than the cytosine residues (73-77%). The computer generated depiction of the triribonucleotide 1 is also shown. These subtle structural features may act as recognition signals for this critical lariat branch site which is essential for the second step in yeast mRNA splicing.

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Section: Conformation Of the Ribose Rings And Handedness Of The Brancsupporting

confidence: 59%

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR

Huss

Gosselin

et al. 1987

Journal of Biomolecular Structure and Dynamics

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“…A strong preference for C2Јendo sugar in 2Ј,5Ј RNA strand is also seen in the energy minimized structure of RNA:2Ј,5Ј RNA hybrid duplex (13). NMR studies on single stranded 2Ј,5Ј di-and tri-nucleosides also show preference for C2Јendo pucker (39,40). Seemingly then, linkage change in RNA from 3Ј,5Ј to 2Ј,5Ј brings about a concomitant change in the preferred conformation of the sugar pucker.…”

Section: Resultsmentioning

confidence: 92%

NMR Structure of a 2′,5′ RNA Favors A Type Duplex with Compact C2′endo Nucleotide Repeat

Premraj

Patel

Kandimalla³

et al. 2001

Biochemical and Biophysical Research Communications

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“…b Coupling constants for protons with lower number are not repeated, spin-spin coupling to P is marked by (P). c From [39], reported data interpolated to 20°C form 9°C and 39°C values. For comparison purposes chemical shifts of H-1′ of Np-are taken as equal.…”

Section: Nmr Analysismentioning

confidence: 99%

Identification of the reaction products of (2′‐5′)oligoadenylate synthetase in the marine sponge

Kuusksalu¹,

Subbi²,

Pehk³

et al. 1998

European Journal of Biochemistry

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Previously we reported on the presence of a high (2′-5′)oligoadenylate synthetase activity in the marine sponge Geodia cydonium [Kuusksalu, A., Pihlak, A., Müller, W. E. G. & Kelve, M. (1995) Eur. J. Biochem. 232, 351Ϫ357]. The presence of (2′-5′)oligoadenylates [(2′-5′)A] in crude sponge extract was shown by radioimmunoassay and by their HPLC comigration with authentic (2′-5′)A oligomers. In addition, the sponge (2′-5′)oligoadenylates displayed biological activity, as determined by inhibition studies of protein biosynthesis in rabbit reticulocyte lysate. In the present study individual (2′-5′)oligoadenylates synthesized by sponge enzyme were separated by HPLC. The exact composition of every oligonucleotide peak eluted was determined by matrix-assisted laser-desorption-ionization mass spectrometry (MALDI-MS) analysis. The 2′-5′ phosphodiester bond in oligoadenylates was verified by NMR analysis. Based on the high concentration of (2′-5′)A oligomers in G. cydonium and their similarity with those found in mammals we propose that the (2′-5′)A system is involved in a cytokine-mediated pathway and/ or in a protection system against viruses, present in the marine environment.Keywords : (2′-5′)oligoadenylate; Geodia cydonium ; matrix-assisted laser-desorption-ionization MS; NMR.Sponges (Porifera) are the simplest multicellular animals, which have existed since the Proteozoic period [1]. In the past few years several cDNA/gene sequences have been isolated and characterized from sponges, especially from the marine demosponge Geodia cydonium. Analyses revealed that sponges contain proteins of the extracellular matrix/basal lamina (e.g. integrin receptor [2], collagen [3] or galectin [4,5]), cell-surface receptors (tyrosine kinase receptor [6]), elements of the sensory system (crystallin [7], metabotropic glutamate receptor [8]) and homologs/modules of an immune system (immunoglobulin-like domains [9], scavenger receptor cysteine-rich domains and short consensus repeats [10], Rh-like protein [11]). These molecules were found to display high similarity to sequences from members of higher metazoan phyla [12].Recently a cDNA encoding a putative cytokine, the endothelial monocyte-activating polypeptide [13], was identified in G. cydonium [14]. The physiological role of this factor in sponges is not known. One pathway in mammalian organisms which is controlled by cytokine(s) is the (2′-5′)oligoadenylate [2′-5′(A)] system. It regulates the RNA degradation pathway and is inCorrespondence to M. Kelve,

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Conformational Analysis of the Nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from Nuclear Magnetic Resonance and Circular Dichroism Studies

Cited by 51 publications

References 37 publications

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR

NMR Structure of a 2′,5′ RNA Favors A Type Duplex with Compact C2′endo Nucleotide Repeat

Identification of the reaction products of (2′‐5′)oligoadenylate synthetase in the marine sponge

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Conformational Analysis of the Nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from Nuclear Magnetic Resonance and Circular Dichroism Studies

Cited by 51 publications

References 37 publications

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A2′p5′G3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from1H-NMR

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A2′p5′G3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from1H-NMR

NMR Structure of a 2′,5′ RNA Favors A Type Duplex with Compact C2′endo Nucleotide Repeat

Identification of the reaction products of (2′‐5′)oligoadenylate synthetase in the marine sponge

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Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR

Structure and Conformation of the Branch Core Triribonucleotide Containing 2′-5′ and 3′-5′ Phosphodiester Linkages (A^2′p5′G_3′p5′C) in Solution, Essential for Yeast mRNA Splicing, Deduced from¹H-NMR