Synthetic spectroscopic models. XIV. Intramolecular stacking interactions between indole and connected nucleic acid bases. Hypochromism and fluorescence

Mutai, Kiyoshi; Gruber, Bruce A.; Leonard, Nelson J.

doi:10.1021/ja00847a038

Cited by 64 publications

(42 citation statements)

References 18 publications

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“…organic solvents having been noted previously for nucleotide base and psoralen (4), indole (14), and quinoline (15) pairs, respectively. The effect of solvents on stacking interaction is not yet completely understood.…”

Section: E Osupporting

confidence: 54%

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Ground and excited-state interactions of coumarin and nucleotide base

Wenska¹,

Paszỳc²

1988

Can. J. Chem.

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GRAZYNA WENSKA and STEFAN PASZYC. Can. J . Chem. 66, 5 13 (1988).Steady-state and time-resolved fluorescence measurements for a series of bichromophoric con~pounds containing 7-methoxycoumarin and nucleotide base residues have been performed in water and in organic solvents. The data from these studies have been used to calculate the relative proportion of folded and extended conformations of bichromophores. Ground-state stacking interactions of coumarin and nucleotide base have been found to be limited to aqueous solution. ' The contribution of the dynamic quenching mechanism to the total fluorescence quenching in water has been estimated. The absence of dynamic quenching in organic solvents isexplained on the basis of the very short lifetime of the fluorophore in methanol.GRAZYNA WENSKA et STEFAN PASZYC. Can. J. Chem. 66, 513 (1988).Operant dans I'eau et dans des solvants organiques, on a mesurC la fluorescence a I'Ctat stationnaire ainsi que celle rCsolue en fonction du temps d'une sCrie de composCs bichromophoriques contenant des rtsidus mCthoxy-7 coumarine et une base nuclCotide. On a utilisC les donntes ainsi obtenues pour calculer les proportions relatives des conformations replite et Ctendue des bichromophores. On a trouve que les interactions d'empilement dans 1'Ctat fondamental de la coumarine et de la base nuclCotide sont IimitCes aux solutions aqueuses. On a t v a l d la contribution du mecanisme de piegeage dynamique au pitgeage total de la fluorescence dans I'eau. On explique l'absence de pitgeage dynamique dans les solvants organiques par le temps de vie tres court du fluorophore dans le methanol.[Traduit par la revue] Introduction It is well known that heteroaromatic compounds from the psoralen family form noncovalent complexes with nucleic acids (1, 2). The formation of the complex by weak forces, i.e., aromatic ring stacking due to hydrophobic and van der Waals forces, is one of several parameters contributing to the overall photobiological activity of psoralens (furocoumarins). The complexation is usually described in terms of the "intercalation model", which predicts that the psoralen molecule is placed between two adjacent nucleotide base pairs. Both ultraviolet absorption and fluorescence spectroscopy can be used to detect the intercalation complex. Its formation is generally accompanied by the bathochromic shift and hypochromicity of the near ultraviolet (uv) absorption band of the psoralen derivative. The fluorescence properties of psoralens also vary upon intercalation. The ability of nucleic acid bases to form such complexes with psoralen has been tested using model compounds in which both interacting molecules were connected with a hydrocarbon chain. The percentage of stacked or folded conformation, as opposed to extended, was determined by the study of the variation of the hypochromic effect with temperature (3, 4).Recently we synthesized a series of compounds containing 7-methoxycoumarin and nucleic acid base: adenine, thymine, and uracil, linked together with a polymethylene chain. ...

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Section: E Osupporting

confidence: 54%

“…Using the approach described previously for the nucleotide base -indole system (14), the fraction y of light absorbed by the extended form of the bichromophoric compound and the fraction a of unfolded conformations of 2-6 in the ground state can be calculated from eqs.…”

Section: Resultsmentioning

confidence: 99%

Ground and excited-state interactions of coumarin and nucleotide base

Wenska¹,

Paszỳc²

1988

Can. J. Chem.

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“…It is also possible that two adenylyl groups on adjacent hexameric rings might interact to prevent the protein from undergoing conformational changes necessary for catalysis. (Indole)-(purine) and (purine)-(purine) stacking interactions + + have been studied extensively with model compounds and in proteins Mutai et al, 1975;Liou & Anderson, 1978). It has been shown that when "caged," fluorescent nucleotides, which have a 1 ,N6 -etheno bridge, are complexed with indoles or tryptophan, their fluorescent properties are changed.…”

Section: Abstract: And-amp; Conformation; Enzyme Activity; Molecular Dymentioning

confidence: 99%

“…The major effect that indole stacking has on &-purine fluorescence is static quenching that results in a "dark" (indole)-(purine) complex with vanishingly small quantum yield. In intramolecular (E-purine)-(indole) complexes, the fraction of complexes in the "dark," stacked complex and in the "open" complex can be determined by measurement of the fluorescence lifetime and the quantum yield of the Epurine Mutai et al, 1975). This model chemistry has prompted the use of E-adenylyl GS as a fluorescent probe of intramolecular (Trp-57)-(adenylyl) interactions in GS.…”

Section: Abstract: And-amp; Conformation; Enzyme Activity; Molecular Dymentioning

confidence: 99%

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Time‐resolved fluorescence and computational studies of adenylylated glutamine synthetase: Analysis of intersubunit interactions

et al. 1993

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Adenylylation of Tyr-397 of each subunit of Escherichia coli glutamine synthetase (GS) down-regulates enzymatic activity in vivo. The overall structure of the enzyme consists of 12 subunits arranged as two hexamers, face to face. Research reported in this paper addresses the question of whether the covalently attached adenylyl group interacts with neighboring amino acid residues to produce the regulatory phenomenon. Wild-type GS has two Trp residues (positions 57 and 158) and the adenylylation site lies within 7-8 A of the Trp-57 loop in the adjacent subunit of the same hexameric ring; Trp-158 is about 35 A from the site of adenylylation. Fluorescence lifetimes and quantum yields have been determined for two fluorophores with wild-type and mutant GS. One fluorophore is E-AMP adenylylated GS (at Tyr-397), and the other fluorophore is the intrinsic protein residue Trp-57. These experiments were conducted in order to detect possible intersubunit interactions between adenylyl groups and the neighboring Trp-57 to search for a role for the Trp-57 loop in the regulation of GS. The fluorescence due to E-AMP of two adenylylated enzymes, wild-type GS and the W158F mutant, exhibits heterogeneous decay kinetics; the data adequately fit to a double exponential decay model with recovered average lifetime values of 18.2 and 2.1 ns, respectively. The pre-exponential factors range from 0.66 to 0.73 for the long lifetime component, at five emission wavelengths. The WS~L-E-AMP enzyme yields longer average lifetime values of 19.5 and 2.4 ns, and the pre-exponential factors range from 0.82 to 0.85 for the long lifetime component. An additional residue in the Trp-57 loop, Lys-58, has been altered and the K58C mutant enzyme has been adenylylated with &-AMP on Tyr-397. Lys-58 is near the ATP binding site and may represent a link by which the adenylyl group controls the activity of GS. The fluorescence of E-AMP-adenylylated K58C mutant GS is best described by a triple exponential decay with average recovered lifetime values of 19.9, 4.6, and 0.58 ns, with the largest fraction being the median lifetime component. Relative quantum yields of ~-AMP-Tyr-397 were measured in order to determine if static quenching occurs from adenine-indole stacking in the wild-type GS. The relative quantum yield of the E-AMP-adenylylated W57L mutant is larger than the wild-type protein by the amount predicted from the difference in lifetime values: thus, no static quenching is evident. Intrinsic tryptophan fluorescence was also studied in the presence and absence of covalently attached adenylyl groups. The fluorescence decay parameters of Trp-57 are not significantly affected by the presence of E-AMP or AMP attached to Tyr-397. Enzymatic activity of the mutant proteins was also studied. The Mg-activated enzymes are nearly completely inhibited upon adenylylation, and regulation is not affected by mutation at Trp-57 or Lys-58. These results indicate that the Trp-57 loop dynamically interacts with the adenylyl group, but a "ring stacked" complex is not f...

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