Indole ring binds to 7‐methylguanine base by π‐π stacking interaction

Kamiichi, Katsuhisa; Danshita, Masaya; Minamino, Naoko; Doi, Mitsunobu; Ishida, Toshimasa; Inoue, Masatoshi

doi:10.1016/0014-5793(86)80129-6

Cited by 20 publications

(15 citation statements)

References 10 publications

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“…The conformation is not dependent on the protonation state of the phosphate groups or on temperature [26]. It should be noted, that while solution structure determinations of m 7 Guo and its nucleotides give a clear and consistent image of the conformational preferences, according to X-ray crystal structures the preferred sugar ring puckering is 2´-endo [28,[30][31][32]. The other conformational parameters are consistent with those observed in solution.…”

Section: Conformation and Intramolecular Interactionssupporting

confidence: 72%

“…Exact population distribution between syn and anti conformers cannot be accurately determined on the basis of NMR-data, but the proportion of anti rotamers appears to be higher with 7-methylguanosine than with guanosine derivatives and phosphorylation of the 5´-position still favors anti rotamers [26], evidently due to electrostatic attraction between the positively charged base and negatively charged phosphate. In X-ray structures obtained in the presence of various amino acids, the dihedral angle about the N-glycosidic bond of m 7 GMP (2a) varies between -103 ° and -105 ° [28,30,32,33].…”

Section: Conformation and Intramolecular Interactionsmentioning

confidence: 99%

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Preparation and Properties of mRNA 5-cap Structure

Mikkola¹,

Salomaki²,

Zhang³

et al. 2005

COC

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The 5´-terminus of eukaryotic messenger RNA (mRNA) molecules contains an unique structure, viz. a dinucleoside 5´,5´-triphosphate moiety where the terminal nucleoside is 7-methylguanosine. This 5´-cap structure serves as a site of recognition for numerous enzymes involved in splicing, transport and translation of mRNA, and protects mRNA against intracellular exonucleases. In addition, viral RNA polymerases use capped mRNA sequences of the host cell as primers for viral RNA synthesis. Understanding of molecular mechanism of all these processes requires detailed information on the chemical properties of the cap structure, including capability to prepare conjugates and structural analogs of the cap for research tools. This review tends to summarize the present knowledge on various aspects of the chemistry of the cap structure, including chemical stability and mechanisms of breakdown, protolytic and complexing equilibria, stacking interactions and synthetic methodology.

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Section: Conformation and Intramolecular Interactionssupporting

confidence: 72%

Section: Conformation and Intramolecular Interactionsmentioning

confidence: 99%

Preparation and Properties of mRNA 5-cap Structure

Mikkola¹,

Salomaki²,

Zhang³

et al. 2005

COC

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“…The vast majority of medicinal agents contain aromatic substituents and their differential recognition by proteins is likely dominated by aromatic-aromatic interactions (8). In biologically related areas of chemistry, aromatic-aromatic interactions are crucially involved in protein-deoxynucleic acid complexes where interactions between aromatic residues and base pairs are seen in x-ray crystal structures (9,10).…”

mentioning

confidence: 99%

π-Stacking Interactions

McGaughey¹,

Gagné²,

Rappé³

1998

Journal of Biological Chemistry

1,049

558

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A representative set of high resolution x-ray crystal structures of nonhomologous proteins have been examined to determine the preferred positions and orientations of noncovalent interactions between the aromatic side chains of the amino acids phenylalanine, tyrosine, histidine, and tryptophan. To study the primary interactions between aromatic amino acids, care has been taken to examine only isolated pairs (dimers) of amino acids because trimers and higher order clusters of aromatic amino acids behave differently than their dimer counterparts. We find that pairs (dimers) of aromatic side chain amino acids preferentially align their respective aromatic rings in an off-centered parallel orientation. Further, we find that this parallel-displaced structure is 0.5-0.75 kcal/mol more stable than a T-shaped structure for phenylalanine interactions and 1 kcal/mol more stable than a T-shaped structure for the full set of aromatic side chain amino acids. This experimentally determined structure and energy difference is consistent with ab initio and molecular mechanics calculations of benzene dimer, however, the results are not in agreement with previously published analyses of aromatic amino acids in proteins. The preferred orientation is referred to as parallel displaced -stacking.Attractive nonbonded interactions between aromatic rings are seen in many areas of chemistry, and hence are of interest to all realms of chemistry. Porphyrin aggregation (1), the conformation of diarylnaphthalenes (2) and phenylacetylene macrocycles (3), and the strength of Kevlar (4) can be attributed, at least in part, to aromatic-aromatic interactions. Aromatic-aromatic interactions have been implicated in catalytic hydroformylation (5), the catalytic formation of elastomeric polypropylene (6), and the asymmetric cis dihydroxylation of olefins (7). The vast majority of medicinal agents contain aromatic substituents and their differential recognition by proteins is likely dominated by aromatic-aromatic interactions (8). In biologically related areas of chemistry, aromatic-aromatic interactions are crucially involved in protein-deoxynucleic acid complexes where interactions between aromatic residues and base pairs are seen in x-ray crystal structures (9, 10).Because aromatic-aromatic interactions are so prevalent across chemistry, a large body of experimental and theoretical work has focused on determining the gas phase structure of the prototype, benzene dimer (11-14, 30). As summarized recently by Sun and Bernstein (15), the experimentally observed structure depends heavily upon the observation technique. Off-centered parallel displaced, 1p, and T-shaped, 1t, structures are the most commonly cited orientations (Structure 1).Large scale ab initio electronic structure theory suggests that the off-centered parallel displaced and T-shaped structures are nearly isoenergetic (11)(12)(13)(14)30). As reported by Sun and Bernstein (15), empirical force field studies favor either off-centered parallel displaced or T-shaped structures depending upon t...

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“…The picture is also complicated by the presence of more than one differently oriented molecule in the unit cell of the P2 1 2 1 2 1 space group (Z = 4). This means that in the case of the tryptammonium cation, a limitation of the IR-LD spectroscopic tool of oriented colloids in nematic liquid crystal suspension is appeared, which prevents a [27]; DOTXUF10 (7-Methylguanosine-5 0 -monophosphate tryptamine trihydrate) [28]; FINZIM ((P)-Tryptamine 4-chlorobenzoic acid) [29]; GANFOQ (Tryptamine 3,4-dimethoxybenzoate) [30]; JOZCOQ (Tryptammonium biphenyl-3-carboxylate) [31]; JOZMEQ (Tryptammonium biphen-4-ylacetate) [31]; LACLOQ (Tryptamine 2-thiophenecarboxylic acid); LACQAH (Tryptamine 3-indoleacetic acid) [32]; TIFLAV (Tryptammonium 3-phenylpropionate) [33]; TRYPIC (Tryptamine picrate) [34]; XIJAP (Tryptamine trans-3-nitrocinnamic acid) [35]; TRPAC (Tryptammonium phenylacetate) [36]; TRYPTA10 (Tryptamine hydrochloride) [37]; WODTUE (Tryptamine trans-cinnamic acid); WODVAM (Tryptamine phenoxyacetic acid); WODVEQ (Tryptamine (phenylthio)acetic acid); WODVIU (Tryptamine 1-naphthylacetic acid); WODVOA (Tryptamine p-nitrocinnamic acid); and WODVUG (Tryptamine diphenylacetic acid) [ presence of a certain assignment to one of the two frequency observed conformers of the molecule in solid state. However, for the vibrational assignment of the characteristic bands to corresponding vibrational modes, the method is apparently unique as far as allowing the investigation of solids independently of their crystalline or amorphous character [12][13][14][15][16][17][18][19][20][21][22].…”

Section: Theoretical Calculationsmentioning

confidence: 97%

Are there preferable conformations of the tryptammonium cation in the solid state? Crystal structure and solid-state linear polarized IR-spectroscopic study of tryptammonium hydrogentartarate

et al. 2007

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Tryptammonium hydrogentartarate (1) crystallizes in the orthorhombic space group P2 1 2 1 2 1 and exhibits a crystal structure consisting of the tryptammonium cation, hydrogentartarate anion and a solvent methanol. The cations and anions are joined into a 3D network by intermolecular NHÁÁÁOH(CH 3 ) and NH 3 ÁÁÁO (tart) bonds with lengths of 2.998, 2.772, 2.902, and 2.847 Å , respectively. Hydrogentartarate anions are themselves connected by strong intermolecular OÁÁÁH-O hydrogen bonds with lengths of 2.481 Å into infinite chains. The anions also participate in moderate hydrogen bonding with solvent methanol molecules of the (tart) OÁÁÁO(CH 3 ) type with bond lengths of 2.736 and 2.762 Å ). The conformational preference of the tryptammonium cation is discussed by comparing the results with the data for other crystallographically determined structures of salts. Quantum chemical calculations at (density functional theory) DFT (B3LYP) level of theory and 6-311++G** basis set are performed for the interacting system tryptammonium cation/H 2 O with a view to predicting the geometry of the most stable conformer. The optical properties of tryptammonium hydrogentartarate have been elucidated in the solid-state by means of linearpolarized solid state IR-spectroscopy (IR-LD) of oriented solids as a colloid suspension in nematic hosts. Some limitations of the method are discussed as well.

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Indole ring binds to 7‐methylguanine base by π‐π stacking interaction

Cited by 20 publications

References 10 publications

Preparation and Properties of mRNA 5-cap Structure

Preparation and Properties of mRNA 5-cap Structure

π-Stacking Interactions

Are there preferable conformations of the tryptammonium cation in the solid state? Crystal structure and solid-state linear polarized IR-spectroscopic study of tryptammonium hydrogentartarate

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