Cross-modulation of the pKa of nucleobases in a single-stranded hexameric-RNA due to tandem electrostatic nearest-neighbor interactions

Journal of the American Chemical Society

Volumn 125, Issue 33, 2003, Pages 9948-9961

  Acharya, P ^a   Acharya, S ^a   Cheruku, P ^a   Amirkhanov, N V ^a   Foldesi A ^a   Chattopadhyaya, J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DEPROTONATION;

CARRIER CONCENTRATION; ELECTROSTATICS; NEGATIVE IONS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH EFFECTS; PROTONS; TITRATION;

RNA;

ADENINE DERIVATIVE; CYTOSINE DERIVATIVE; GUANOSINE PHOSPHATE; NUCLEIC ACID BASE; NUCLEOTIDE; PHOSPHATE; PROTON; RNA; OLIGORIBONUCLEOTIDE; THIOL DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; ELECTRICITY; ELECTRON; ELEMENTARY PARTICLE; NUCLEAR MAGNETIC RESONANCE; PH; PROTON TRANSPORT; REACTION ANALYSIS; STRUCTURE ANALYSIS; TITRIMETRY; CHEMISTRY; CONFORMATION; KINETICS; THERMODYNAMICS;

5'-GUANYLIC ACID; ELECTROSTATICS; HYDROGEN-ION CONCENTRATION; KINETICS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; OLIGORIBONUCLEOTIDES; RNA; SULFHYDRYL COMPOUNDS; THERMODYNAMICS;

EID: 0041519414     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja034651h     Document Type: Article

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50. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
51. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
52. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
53. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
54. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
55. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
56. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
57. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
58. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
59. Studies showing the importance of the weak noncovalent aromatic interactions in biological functionalities: (a) McFail-Isom, L.; Shui, X.; Williams, L. D. Biochemistry 1998, 37, 17105. (b) Rooman, M.; Liévin, J. ; Buisine. E.; Wintjens R. J. Mol. Biol. 2002, 319, 67. (c) Umezawa, Y.; Nishio, M. Nucleic Acids Res. 2002, 30, 2183. (d) Zacharias, N.; Dougherty, D. Trends Pharm. Sci. 2002, 23, 281 and references therein. (e) Boehr, D. D.; Farley, A. R.; Wright, G. D.; Cox, J. R. Chem. Biol. 2002, 9, 1209. (f) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372. (g) Butterfield, S. M.; Patel, P. R.; Water, M. L. J. Am. Chem. Soc. 2002, 124, 9751. (h) Tsou, L. K.; Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 14917. (i) Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. Proteins: Struct., Funct., Genet. 2002, 48, 117. (j) Zhou, Z.; Swenson, R. P. Biochemistry 1996, 35, 15980. (k) Gallivan, J. P.; Dougherty, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459. (l) Biot, C.; Buisine, E.; Kwasigroch, J.-M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816.
60. The intra- and intermolecular stacking and/or other aromatic interactions involving both biological as well as nonbiological systems has been shown to be a major force in molecular recognition and biological functionalities. The aromatic stacking interaction between nucleobases in water has been implicated to electrostatic effects (dipole-dipole and dipole-induced dipole) interactions, dispersion (momentary dipole-induced dipole), and solvation. Hunter et al. invoked offset stacking involving attractive atom-πσ interaction (electrostatic in nature) and edge-to-face interactions (same as center-to-edge termed by Siegel et al.) rather than energetically unfavorable π-π interaction as in face-to-face stacking between two aromatic moieties. In both offset stacking and edge-to-face interactions, the CH group of the edge ring and the electron density of the face ring are sensitive to changes in the local charge (partial charge) distribution of the two rings. However, unlike offset stacking, edge-to-face interaction is considered as weak noncovalent through-space aromatic interaction, not any stacking interaction. Theoretical studies recently showed that dispersion effects other than electrostatics dominate both aryl CH-π, and alkyl CH-π interactions. In all cases alkyl CH-π interactions are weaker than aryl CH-π interactions. Nishio et al. proposed partial charge transfer arising from through-space proximity between alkyl hydrogen and aromatic moiety as the basis for CH-π interaction. On the other hand, Siegel et al. and Diedrich et al. proposed a through-space polar (Coulombic)/π contribution as a dominating factor in the electrostatic interactions involved in edge-to-face as well as the center-to-edge (i.e., offset) oriented aromatic moieties in the neutral as well as in the ionic states (such as carboxylate ion/arene and trimethylammonium ion/arene interaction). Moreover, Dougherty et al. showed that both electrostatic and polarization effects are dominant contributions in the cation-π interaction, which have been shown to make a significant contribution in the stabilization of α-helical peptides in aqueous solution. Recent works have also shown theoretical evidences of anion-π interactions.
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91. 3p in pentamer 7 in comparison with the hexamer 8, Figure 3). This also means that the pseudoaromaticity of the triplet codon, independent of the RNA chain length, is maximally cross-modulated owing to their full electronic coupling with the nearest neighbor. Clearly, the last three nucleobases at the 3′-end of the hexamer 8 are sensing the electrostatic interaction owing to the anionic character of 9-guaninyl moiety to a much lesser extent (ca. 10-15%) compared to the first two nucleobases after 5′-Gp anion. This is because of the fact that the attractive Coulombic forces stabilize the stacked state of the hexamer more efficiently than in the pentamer. As a result, this stabilizing atom-πσ interaction counteracts the destabilizing anion-π interaction more efficiently in the former than in the latter.
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