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  • 1. Acharya, P.
    et al.
    Acharya, S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A.
    Chattopadhyaya, J.
    Tandem Electrostatic Effect from the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-Neighbor Interaction2003Ingår i: J. Am. Chem. Soc, Vol. 125, s. 2094-2100Artikel i tidskrift (Refereegranskat)
  • 2.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction.2003Ingår i: J Am Chem Soc, ISSN 0002-7863, Vol. 125, nr 8, s. 2094-100Artikel i tidskrift (Övrigt vetenskapligt)
  • 3.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Institutionen för cell- och molekylärbiologi, Bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Institutionen för cell- och molekylärbiologi, Bioorganisk kemi.
    Electrostatic Cross-modulation of the Pseudoaromatic Character in Single Stranded RNA by Nearest-neighbor interactions2005Ingår i: Pure and Applied Chemistry, Vol. 77, nr 1, s. 291-311Artikel i tidskrift (Refereegranskat)
  • 4.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate.2002Ingår i: J. Org. Chem., Vol. 67, s. 1852-1865Artikel i tidskrift (Refereegranskat)
  • 5. Acharya, P.
    et al.
    Cheruku, P.
    Chatterjee, S.
    Acharya, S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J.
    Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes2004Ingår i: J. Am. Chem. Soc., Vol. 126, s. 2862-2869Artikel i tidskrift (Refereegranskat)
  • 6.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Cheruku, P
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chatterjee, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes.2004Ingår i: J Am Chem Soc, ISSN 0002-7863, Vol. 126, nr 9, s. 2862-9Artikel i tidskrift (Övrigt vetenskapligt)
  • 7.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Cheruku, P
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chatterjee, Sunanda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Karthick Babu, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes2004Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, nr 9, s. 2862-2869Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by (1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK(a) values of the monomeric nucleotide blocks as well as Delta pK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G*(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimics to expand the alphabet of the genetic code.

  • 8.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Issakson, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Pradeepkumar, P.I.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Experimental Evidences Unequivocally Prove the Role of Stereoelectronics as One of the Major Forces Responsible for the Self-assembly of DNA and RNA.2002Ingår i: Collect. Czech. Chem. Commun.: Collection Symposium Series (Chemistry of Nucleic Acid Components), Vol. 5, s. 99-120Artikel i tidskrift (Refereegranskat)
  • 9.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Nawrot, B
    Sprinzl, M
    Thibaudeau, C
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    The strength of the 3 '-gauche effect dictates the structure of 3 '-O-anthraniloyladenosine and its 5 '-phosphate, two analogues of the 3 '-end of aminoacyl-tRNA1999Ingår i: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, ISSN 0300-9580, nr 7, s. 1531-1536Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Anthranilic acid charged yeast tRNA(Phe) or E. Coli tRNA(Val) are able to form a stable complex with EF-Tu*GTP, hence the 2'- and 3'-O-anthraniloyladenosines and their 5'-phosphate counterparts have been conceived to be the smallest units that are capable

  • 10.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Plashkevych, O
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Morita, C
    Yamada, S
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.2003Ingår i: J Org Chem, ISSN 0022-3263, Vol. 68, nr 4, s. 1529-38Artikel i tidskrift (Övrigt vetenskapligt)
  • 11.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Thibaudeau, C
    Chattopadhyaya, J
    An energetic correlation of ab initio and NMR studies of the 3 '-gauche effect in 3 '-substituted thymidines2001Ingår i: NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, ISSN 1525-7770, Vol. 20, nr 4-7, s. 1229-1233Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A straightforward correlation of our experimental NMR findings on 3'-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the DeltaG(NRM)degrees (298k) of N reversible arrow S equilibrium in nucleoside can be predicted

  • 12.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Trifonova, A
    Thibaudeau, C
    Foldesi, A
    Chattopadhyaya, J
    The transmission of the electronic character of guanin-9-yl drives the sugar-phosphate backbone torsions in guanosine 3 ',5 '-bisphosphate1999Ingår i: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, ISSN 1433-7851, Vol. 38, nr 24, s. 3645-3650Artikel i tidskrift (Refereegranskat)
  • 13.
    Acharya, P
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Velikian, I
    Acharya, S
    Chattopadhyaya, J
    Molecular modelling of 2 '-OH mediated hydrogen bonding in ribonucleos(t)ides by NMR constrained AM1 and MMX calculations2001Ingår i: NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, ISSN 1525-7770, Vol. 20, nr 4-7, s. 1211-1217Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The intra- and intermolecular hydrogen bonding (DeltaG(298K)degrees approximate to 2 kcal mol(-1)) of 2'-OH in nucleos(t)ides has been reported by the temperature- and concentration-dependent NMR study in conjunction with dihedral dependence of the NMR de

  • 14.
    Acharya, Parag
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA2003Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl adenosine (a mimic of 3'-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl adenosine, thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

    Delarbeten
    1. The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
    Öppna denna publikation i ny flik eller fönster >>The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
    Visa övriga...
    1999 Ingår i: Angew. Chem. Int. Ed., Vol. 38, nr 24, s. 3645-3650Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91143 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    2. The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
    Öppna denna publikation i ny flik eller fönster >>The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
    Visa övriga...
    2000 Ingår i: J. Phys. Org. Chem., Vol. 13, s. 300-305Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91144 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    3. The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
    Öppna denna publikation i ny flik eller fönster >>The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
    Visa övriga...
    1999 Ingår i: J. Chem. Soc. Perkin 2, s. 1531-1536Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91145 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    4. The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    Öppna denna publikation i ny flik eller fönster >>The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    2002 Ingår i: J. Org. Chem., Vol. 67, nr 6, s. 1852-1865Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91146 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    5. A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
    Öppna denna publikation i ny flik eller fönster >>A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
    Visa övriga...
    2003 Ingår i: J. Org. Chem., Vol. 68, nr 4, s. 1529-1538Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91147 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    6. Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    Öppna denna publikation i ny flik eller fönster >>Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    2002 Ingår i: J. Am. Chem. Soc., Vol. 124, nr 46, s. 13722-13730Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91148 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    7. Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    Öppna denna publikation i ny flik eller fönster >>Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    2003 Ingår i: J. Am. Chem. Soc., Vol. 125, nr 8, s. 2094-2100Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-91149 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    8. Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Öppna denna publikation i ny flik eller fönster >>Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
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    2003 (Engelska)Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, nr 33, s. 9948-9961Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-91150 (URN)10.1021/ja034651h (DOI)12914458 (PubMedID)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    9. The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
    Öppna denna publikation i ny flik eller fönster >>The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
    Visa övriga...
    Ingår i: J. Am. Chem. Soc.Artikel i tidskrift (Refereegranskat) Submitted
    Identifikatorer
    urn:nbn:se:uu:diva-91151 (URN)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26Bibliografiskt granskad
    10. Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
    Öppna denna publikation i ny flik eller fönster >>Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
    Visa övriga...
    2004 (Engelska)Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, nr 9, s. 2862-2869Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by (1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK(a) values of the monomeric nucleotide blocks as well as Delta pK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G*(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimics to expand the alphabet of the genetic code.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-91152 (URN)10.1021/ja0386546 (DOI)14995203 (PubMedID)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
  • 15.
    Acharya, Parag
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, Sandipta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Cheruku, P
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Amirkhanov, N. V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions2003Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, nr 33, s. 9948-9961Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

  • 16.
    Acharya, S.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, P.
    Földesi, A.
    Chattopadhyaya, J.
    Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State2002Ingår i: J. Am. Chem. Soc., Vol. 124, s. 13722-13730Artikel i tidskrift (Refereegranskat)
  • 17.
    Acharya, S
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Acharya, P
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Cross-modulation of physicochemical character of aglycones in dinucleoside (3'-->5') monophosphates by the nearest neighbor interaction in the stacked state.2002Ingår i: J Am Chem Soc, ISSN 0002-7863, Vol. 124, nr 46, s. 13722-30Artikel i tidskrift (Övrigt vetenskapligt)
  • 18.
    Acharya, S.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Barman, J.
    Cheruku, P.
    Chatterjee, S.
    Acharya, P.
    Isaksson, J.
    Chattopadhyaya, J.
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004Ingår i: J. Am. Chem. Soc., Vol. 126, s. 8674-8681Artikel i tidskrift (Refereegranskat)
  • 19.
    Acharya, S.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A.
    Chattopadhyaya, J.
    The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates2003Ingår i: J. Org. Chem., Vol. 68, s. 1906-1910Artikel i tidskrift (Refereegranskat)
  • 20.
    Acharya, S
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Földesi, A
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    The pK(a) of the internucleotidic 2'-hydroxyl group in diribonucleoside (3'-->5') monophosphates.2003Ingår i: J Org Chem, ISSN 0022-3263, Vol. 68, nr 5, s. 1906-10Artikel i tidskrift (Övrigt vetenskapligt)
  • 21.
    Acharya, Sandipta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Some Aspects of Physicochemical Properties of DNA and RNA2006Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pKa values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pKa values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.

    Delarbeten
    1. The pKa’s of 2'-Hydroxyl Group in Nucleosides and Nucleotides
    Öppna denna publikation i ny flik eller fönster >>The pKa’s of 2'-Hydroxyl Group in Nucleosides and Nucleotides
    Visa övriga...
    2001 Ingår i: J. Am. Chem. Soc., Vol. 123, s. 2893-2894Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94240 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07 Senast uppdaterad: 2014-03-03Bibliografiskt granskad
    2. The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates
    Öppna denna publikation i ny flik eller fönster >>The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates
    2003 Ingår i: J. Org. Chem., Vol. 68, s. 1906-1910Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94241 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    3. Non-identical electronic characters of the internucleotidic pohosphates in RNA modulate the chemical reactivity of the phosphodiester bonds
    Öppna denna publikation i ny flik eller fönster >>Non-identical electronic characters of the internucleotidic pohosphates in RNA modulate the chemical reactivity of the phosphodiester bonds
    Visa övriga...
    2006 Ingår i: Org. Biomol. Chem., Vol. 4, s. 928-941Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94242 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    4. Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State
    Öppna denna publikation i ny flik eller fönster >>Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State
    2002 Ingår i: J. Am. Chem. Soc., Vol. 124, s. 13722-13730Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94243 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    5. Tandem Electrostatic Effect from the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-Neighbor Interaction
    Öppna denna publikation i ny flik eller fönster >>Tandem Electrostatic Effect from the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-Neighbor Interaction
    2003 Ingår i: J. Am. Chem. Soc, Vol. 125, s. 2094-2100Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94244 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    6. Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Öppna denna publikation i ny flik eller fönster >>Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Visa övriga...
    2003 (Engelska)Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, nr 33, s. 9948-9961Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-91150 (URN)10.1021/ja034651h (DOI)12914458 (PubMedID)
    Tillgänglig från: 2003-11-26 Skapad: 2003-11-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    7. Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
    Öppna denna publikation i ny flik eller fönster >>Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
    Visa övriga...
    2004 Ingår i: J. Am. Chem. Soc., Vol. 126, s. 8674-8681Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94246 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    8. Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern
    Öppna denna publikation i ny flik eller fönster >>Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern
    Visa övriga...
    2004 Ingår i: Biochemistry, Vol. 43, s. 15996-16010Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94247 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
    9. Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
    Öppna denna publikation i ny flik eller fönster >>Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
    Visa övriga...
    2004 Ingår i: J. Am. Chem. Soc., Vol. 126, s. 2862-2869Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94248 (URN)
    Tillgänglig från: 2006-04-07 Skapad: 2006-04-07Bibliografiskt granskad
  • 22. Acharya, Sandipta
    et al.
    Barman, Jharna
    Cheruku, Pradeep
    Chatterjee, Subhrangsu
    Acharya, Parag
    Isaksson, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Chattopadhyaya, Jyoti
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004Ingår i: J. Am. Chem. Soc., ISSN 0002-7863, Vol. 126, s. 8674-8681Artikel i tidskrift (Refereegranskat)
  • 23.
    Acharya, Sandipta
    et al.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för bioorganisk kemi.
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, nr 28, s. 8674-8681Artikel i tidskrift (Refereegranskat)
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    Chattopadhyaya, J
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi.
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    Abstract [en]

    The different extent of the target RNA cleavage at t(99.9%) by RNase H in the AON-RNA duplexes, at the RNA saturation condition by antisense oligo, is due to different recognition and catalytic properties of RNase H toward the hybrids owing to different s

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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Kemiska sektionen, Institutionen för biokemi och organisk kemi, Biokemi.
    Zhou, Chuanzheng
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Kemiska sektionen, Institutionen för biokemi och organisk kemi, Biokemi.
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Kemiska sektionen, Institutionen för biokemi och organisk kemi, Biokemi.
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    Medicinska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Kemiska sektionen, Institutionen för biokemi och organisk kemi, Biokemi.
    Chattopadhyaya, Jyoti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för bioorganisk kemi. Kemiska sektionen, Institutionen för biokemi och organisk kemi, Biokemi.
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