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Cherepanov AV, Glaubitz C, Schwalbe H. High-resolution studies of uniformly 13C,15N-labeled RNA by solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2010; 49:4747-50. [PMID: 20533472 DOI: 10.1002/anie.200906885] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alexey V Cherepanov
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438 Frankfurt, Germany
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2
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Cherepanov A, Glaubitz C, Schwalbe H. Hochauflösende Festkörper-NMR-Spektroskopie an vollständig 13C,15N-markierter RNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906885] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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3
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Fischer JT, Reinscheid UM. 13C Chemical Shifts and1JCH Coupling Constants of Cytidine at Differentχ Dihedrals Based on DFT Calculations. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Sychrovský V, Müller N, Schneider B, Smrecki V, Spirko V, Sponer J, Trantírek L. Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA. J Am Chem Soc 2006; 127:14663-7. [PMID: 16231919 DOI: 10.1021/ja050894t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dependence of N1/9 and C1' chemical shielding (CS) tensors on the glycosidic bond orientation (chi) and sugar pucker (P) in the DNA nucleosides 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on chi and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1'-H1' dipole-dipole (Ravindranathan et al. J. Biomol. NMR 2003, 27, 365-75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962-70) and highlight possible limitations of these methods when applied to DNA.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
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5
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Boudreau EA, Pelczer I, Borer PN, Heffron GJ, LaPlante SR. Changes in drug 13C NMR chemical shifts as a tool for monitoring interactions with DNA. Biophys Chem 2004; 109:333-44. [PMID: 15110931 DOI: 10.1016/j.bpc.2003.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 11/11/2003] [Accepted: 12/11/2003] [Indexed: 10/26/2022]
Abstract
The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to monitor drug 13C NMR chemical shifts changes. The binding mode of netropsin to the minor groove of DNA is well-known, and served as a good model for evaluating the relative sensitivity of 13C chemical shifts to hydrogen bonding. Large downfield shifts were observed for four resonances of carbons that neighbor sites which are known to form hydrogen bond interactions with the DNA minor groove. Many of the remaining resonances of netropsin exhibit shielding or relatively smaller deshielding changes. Based on the model system presented here, large deshielding NMR shift changes of a ligand upon macromolecule binding can likely be attributed to hydrogen bond formation at nearby sites.
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Affiliation(s)
- Eilis A Boudreau
- Health Science Research and Development Program, Portland VA Medical Center, Portland, OR 97239, USA
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6
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Fadrná E, Koca J. Conformational flexibility of two RNA trimers explored by computational tools and database search. J Biomol Struct Dyn 2003; 20:715-32. [PMID: 12643774 DOI: 10.1080/07391102.2003.10506888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data. Registry numbers: adenylyl-(3' --> 5')-adenylyl-(3' --> 5')-adenosine [917-44-2] adenylyl-(3' --> 5')-uridylyl-(3' --> 5')-guanosine [3494-35-7].
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Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Department of Organic Chemistry, Faculty of Science, Masaryk University, Kotlrsk 2, 611 37 Brno, Czech Republic.
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7
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LaPlante SR, Borer PN. Changes in 13C NMR chemical shifts of DNA as a tool for monitoring drug interactions. Biophys Chem 2001; 90:219-32. [PMID: 11407640 DOI: 10.1016/s0301-4622(01)00143-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to explore the effects of ligand binding on the 13C NMR chemical shifts of the DNA base and sugar carbons. The binding mode of netrospin to TA-rich tracts of DNA has been well documented and served as an attractive model system. For the base carbons, four large changes in resonance chemical shifts were observed upon complex formation: -0.64 ppm for carbon 4 of either Ado4 or Ado6, 1.36 ppm for carbon 2 of Thd5, 1.33 ppm for carbon 5 of Thd5 and 0.94 for carbon 6 of Thd5. AdoC4 is covalently bonded to a heteroatom that is hydrogen bonded to netropsin; this relatively large deshielding is consistent with the known hydrogen bond formed at AdoN3. The three large shielding increases are consistent with hydrogen bonds to water in the minor groove being disrupted upon netropsin binding. For the DNA sugar resonances, large changes in chemical shifts were observed upon netropsin complexation. The 2', 3' and 5' 13C resonances of Thd3 and Thd5 were shielded whereas those of Ado4 and Ado6 were deshielded; the 13C resonances of 1' and 4' could not be assigned. These changes are consistent with alteration of the dynamic pseudorotational states occupied by the DNA sugars. A significant alteration in the pseudorotational states of Ado4 or Ado6 must occur as suggested by the large change in chemical shift of -1.65 ppm of the C3' carbon. In conclusion, 13C NMR may serve as a practical tool for analyzing structural changes in DNA-ligand complexes.
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Affiliation(s)
- S R LaPlante
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, PQ.
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8
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Hayes MP, Hatala PJ, Sherer BA, Tong X, Zanatta N, Borer PN, Kallmerten J. Regioselective synthesis of 13C1-labeled 2-deoxyribonolactones. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)01148-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Hosono K, Hosaka H, Kawai G, Takai K, Takaku H. The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:374-82. [PMID: 10673038 DOI: 10.1016/s0167-4781(99)00215-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We studied the hairpin-loop structure of an RNA fragment (GUUUCGUACAAAC) (R13) with the sequence corresponding to the self-cleavage domain in the precursor of an RNA molecule from bacteriophage T4-infected Escherichia coli cells (p2Sp1 RNA). In order to determine the influence of the hairpin-loop structure on these sequence-specific cleavage reactions, we have synthesized oligoribonucleotides containing hairpin-loop, double-helical stem-loop, and single-stranded RNA structures. The cleavage was affected by the hairpin-loop structure. Furthermore, the helix-stem, which retains the thermodynamically extrastable stem hairpin-loop structures, is also important for the cleavage activity. However, the thermodynamically extrastable helix-stem structure reduced the cleavage activity of the adjacent UA and CA sequences at the helix-stem site. For the cleavage reactions of the RNA cleavage products, the R6 (ACAAAC), R7 (GUUUCGU), and R9 (GUUUCGUAC) mers from the parent RNA, R13 (GUUUCGUACAAAC), a very slight amount of cleavage product (2%) from the RNA 9 was observed, but no reaction occurred for the R6 and R7. We also describe the influences of the sequences (UA and CA) on the cleavage activity.
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Affiliation(s)
- K Hosono
- Department of Industrial Chemistry and High Technology Research Center, Chiba Institute of Technology, Narashino, Japan
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10
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Koca J. Travelling through conformational space: an approach for analyzing the conformational behaviour of flexible molecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:137-73. [PMID: 9785960 DOI: 10.1016/s0079-6107(98)00029-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The applications of the single-co-ordinate-driving (SCD) method in conformational analysis of flexible molecules have been discussed. SCD can best be characterised as travelling through low energy areas of the conformational space. It has been shown that SCD provides detailed information about the conformational behaviour of small and middle sized flexible molecules. It has been demonstrated that SCD may fail for molecules which are more rigid but still conformationally interesting, for example, AUG trimer of RNA. It has been found out that the search problems are eliminated when SCD is coupled with simulated annealing (SCD-SA). Both SCD and SCD-SA methods may be recognised as successful tools for analysis of conformational space. It has been demonstrated, how SCD and SCD-SA results can be used as a background to discover and analyse correlated conformational processes, to quantify molecular conformational flexibility, and to provide an appropriate background for an efficient free energy simulation.
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Affiliation(s)
- J Koca
- Department of Organic Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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11
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Dejaegere AP, Case DA. Density Functional Study of Ribose and Deoxyribose Chemical Shifts. J Phys Chem A 1998. [DOI: 10.1021/jp980926h] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annick P. Dejaegere
- Groupe RMN-UPR 9003, Ecole Supérieure de Biotechnologie de Strasbourg, 67400 Illkirch, France, and Lab. de Chimie Biophysique, ISIS-UPRESA-7006 CNRS, rue B. Pascal, 67000 Strasbourg, France
| | - David A. Case
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92307
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12
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Fadrná E, Koča J. Single-Coordinate-Driving Method Coupled with Simulated Annealing. An Efficient Tool To Search Conformational Space. J Phys Chem B 1997. [DOI: 10.1021/jp9710695] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Eva Fadrná
- Department of Organic Chemistry and Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- Department of Organic Chemistry and Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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13
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Fadrná E, Koča J. A combination of driving method with simulated annealing to search conformational space. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(96)05004-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Norberg J, Nilsson L. Conformational Free Energy Landscape of ApApA from Molecular Dynamics Simulations. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952950q] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Norberg
- Center for Structural Biochemistry, Department of Biosciences at Novum, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Lennart Nilsson
- Center for Structural Biochemistry, Department of Biosciences at Novum, Karolinska Institutet, S-141 57 Huddinge, Sweden
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15
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Bouchemal-Chibani N, Lebrun A, Hervé du Penhoat C, Ghomi M, Laigle A, Derouet C, Turpin PY. Thermodynamic and structural properties of r(ACC) as revealed by ultraviolet electronic absorption, circular dichroism, 1H-NMR spectroscopy and Monte Carlo simulations. J Biomol Struct Dyn 1994; 12:695-724. [PMID: 7727067 DOI: 10.1080/07391102.1994.10508768] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UV absorption, circular dichroism (CD) and 1H NMR, associated with Monte Carlo (MC) molecular structure simulations have been applied to the study of the trinucleoside diphosphate: r(ACC). The MC study which has been conducted as a function of temperature, is based on random variations of the nucleotide conformational angles, i.e. phosphodiester chain torsional angles and sugar pucker pseudorotational angles. All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker. Six different initial structures have been selected in order to explore the molecular conformational space as completely as possible. This simulation procedure led to distinct families of equilibrium conformations at 283, 298 and 318 K. The thermodynamical parameters such as variations in entropy, enthalpy and also melting temperature (delta SX0, delta HX0 and Tm) of the stacking (X) equilibrium were obtained from UV absorption and circular dichroism (CD) spectra recorded over a 80K temperature range. Chemical shifts (delta), vicinal coupling constants (3Jk,l), and cross-relaxation rate (sigma k,l) of trimers were measured at 400.13 MHz over a range of concentrations (2-13 mM) and temperatures (283-333K). Least-squares fitting of the experimental chemical shifts to simple models of association (A) and stacking equilibria allowed separation of the variations in the delta values (delta delta X and delta delta A) due to either phenomenon. The three NMR data sets (delta delta X, 3Jk,l, and sigma k,l) were then evaluated for the minima conformers obtained with the MC stimulations. Theoretical values of delta delta X were estimated using the results of an ab initio study while the coupling constant data were simulated with Karplus-type equations. Finally, the relaxation data were simulated from the distance matrices using treatment for cases of both slow conformational exchange accompanied by rapid small-amplitude fluctuations about the minima structures. A consistent picture of the large amplitude deformations (torsional angle variation) of these trimers has emerged from the present study. Optimized conformational blends at 283,296 and 318K were obtained by least-squares fitting of the experimental data to the theoretical ones, while considering the populations as adjustable parameters. As it would be expected, the right-handed helical conformation (A-RNA type) is found to be the major stacked species, in the temperature range of 283 to 318K. Limited evidence for bulged structures has been obtained, whereas novel reverse-stacked and half-stacked conformers also presented theoretical data compatible with the NMR observables of aqueous r(ACC).
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16
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Ghomi M, Victor JM, Henriet C. Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers. J Comput Chem 1994. [DOI: 10.1002/jcc.540150407] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Abstract
The chemical stability of phosphodiester bonds of some oligoribonucleotides in the presence of a cofactor like polyvinylpyrolidine (PVP) is sequence dependent. It was found that pyrimidine-A (YA) and pyrimidine-C (YC) are especially susceptible to hydrolysis. The hydrolyzability of this same phosphodiester bond is dependent on its position in the oligomer. The presence of 3' and 5'-adjacent nucleotides enhances hydrolysis of the UA phosphodiester bond. The acceleration of the hydrolysis of UA by a 5'-adjacent nucleotide is not base dependent. However, a 3'-adjacent purine increases hydrolysis of a UA phosphodiester bond more than a 3'-pyrimidine. The presence of the exoamino group on the 3'-side base (on 6 and 4 position for adenosine and cytidine, respectively) of YA or YZ phosphodiester bond is required for hydrolysis.
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Affiliation(s)
- R Kierzek
- Department of Chemistry, University of Rochester, NY 14627-0216
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18
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Abstract
Selective cleavage of phosphodiester bonds in RNA is important in the processing of large RNA molecules. This paper reports specific cleavage at UA sequences in single stranded oligoribonucleotides as short as hexamers. The hydrolysis between U and A leaves a 2',3'-cyclic phosphate on the 5'-side and a 5'-hydroxyl group on the 3' side of the cleavage. The hydrolysis is promoted by a wide range of cofactors, including polymeric organic compounds such as polyvinylpyrrolydone (PVP) and by proteins. A variety of experiments suggests the cleavage is not due to contamination by ribonuclease. The rate of cleavage is a function of oligoribonucleotide, PVP and spermidine concentrations. Mg2+ is not required. The phenomenon described here can potentially provide a relatively simple way of coding chemical stability into single stranded RNA based on its sequence and structure. This process seems to be similar to that involved in post-transcriptional degradation of mRNA.
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Affiliation(s)
- R Kierzek
- Department of Chemistry, University of Rochester, NY 14627-0216
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19
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Abstract
RNA molecules perform a wide variety of biological functions, from enzymic activity to storage and propagation of genetic information.
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Affiliation(s)
- G Varani
- Department of Chemistry, University of California, Berkeley 94720
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20
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Orban J, Bell RA. 1H NMR assignments and conformational analysis of the oligoribonucleotides CA, CAU, CAUG, ACAUG, and UCAUG: observation of pyrimidine H5-H1' long-range scalar couplings. J Biomol Struct Dyn 1990; 7:837-48. [PMID: 2310518 DOI: 10.1080/07391102.1990.10508527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conformational analysis and 1H NMR spectral assignments have been carried out using COSY and RELAY methods for a series of related oligoribonucleotides including two pentamers with 5'-dangling bases. Intraresidue long-range five bond scalar coupling was observed between pyrimidine H5 and H1' protons in the COSY-45 spectra and this feature was useful for both assignment purposes and conformational analysis. The ribose ring conformations were predominantly C3'-endo with the C2'-endo population increasing at the 3'-terminus. The 5'-dangling bases were not stacked efficiently, exhibiting lower % C3'-endo values than their 3'-nearest neighbors. Backbone torsion angle population. beta t, gamma +, epsilon t, were determined using 1H-1H, 1H-31P, and 13C-31P coupling constants. From beta t and gamma + populations the U3-G4 step in CAUG was found to be less efficiently stacked than the C1-A2 and A2-U3 steps. This observation in solution is consistent with the fiber diffraction A-RNA model (S. Arnott, D.W.L. Hukins, S.D. Dover, W. Fuller and A.R. Hodgson, J. Mol. Biol. 81, 107-122, 1973) which also predicts poor stacking in a U-G dinucleotide. The epsilon t populations were greater than 65% for all C3'-O3' bonds and consistent with a right-handed A-RNA helix.
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Affiliation(s)
- J Orban
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada
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21
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Borer PN, LaPlante SR, Zanatta N, Levy GC. Hydrogen-bonding effects and 13C-NMR of the DNA double helix. Nucleic Acids Res 1988; 16:2323-32. [PMID: 3357779 PMCID: PMC338219 DOI: 10.1093/nar/16.5.2323] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
13C-nmr chemical shifts of the nucleotides in DNA are sensitive to hydrogen bonding, especially for three of the carbons immediately bonded to exocyclic oxygen or nitrogen atoms acting as H-bond acceptors or donors. GuoC2, GuoC6 and ThdC4 are strongly deshielded (about 1 ppm) upon Watson-Crick pairing in oligodeoxynucleotide duplexes, regardless of the base sequence. Deshielding at these sites may be useful to distinguish bases involved in Watson-Crick pairs from unpaired bases.
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Affiliation(s)
- P N Borer
- NIH Research Resource, Syracuse University, NY 13244-1200
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22
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van den Hoogen YT, Treurniet SJ, Roelen HC, de Vroom E, van der Marel GA, van Boom JH, Altona C. Conformational analysis of the tetranucleotides m6(2)A-m6(2)A-U-m6(2)A(m6(2)A = N6-dimethyladenosine) and U-m6(2)A-U-m6(2)A and of the hybrid dA-r(U-A). A one- and two-dimensional NMR study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 171:155-62. [PMID: 3123229 DOI: 10.1111/j.1432-1033.1988.tb13771.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A 1H-NMR investigation was carried out on the tetranucleotides U-m6(2)A-U-m6(2)A and m6(2)A-m6(2)A-U-m6(2)A (m6(2) = N6-dimethyladenosine) as well as on the hybrid trinucleotide dA-r(U-A). An extensive comparison with m6(2)A-U-m6(2)A and other relevant compounds is made. Previous proton NMR studies on trinucleotides have shown that purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as a common feature that the interior pyrimidine residue bulges out, whereas the flanking purine residues stack upon each other. A stacking interaction on the 3' side of the bulge is known to have no measurable effect on the bulge population. Chemical-shift data, ribose ring conformational analysis and information from NOE experiments now show unambiguously that the moderate U(1)-m6(2)A(2) stack in U-m6(2)A-U-m6(2)A diminishes the population of bulged-out structures in favour of a regular stack. This tendency towards conformational transmission in the downstream 5'----3' direction is fully confirmed by the fact that the strong m6(2)A(1)-m6(2)A(2) stack in the tetranucleotide m6(2)A-m6(2)A-U-m6(2)A virtually precludes the formation of bulged-out structures. The conformational characteristics of dA-r(U-A) appear comparable with those of m6(2)A-U-m6(2)A, which indicates that the presence of a 2'-hydroxyl group in the first purine residue is not a necessary prerequisite for the formation of a bulge.
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23
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van den Hoogen YT, Lankhorst PP, Gijsman P, Hartel AJ, van Boom JH, Altona C. Conformational analysis of the dinucleotides 5'-methylphospho-N6-dimethyladenylyl-uridine (mpm62A-U) and 5'methylphospho-uridylyl-N6-dimethyladenosine (mpU-m62A) and of the trinucleotide U-m62A-U. A nuclear magnetic resonance and circular dichroic study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 171:143-53. [PMID: 3123228 DOI: 10.1111/j.1432-1033.1988.tb13770.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
NMR and CD studies were carried out on the dinucleotides 5'-methylphospho-N6-dimethyladenylyl-uridine (mpm62-U) and 5'-methylphospho-uridylyl-N6-dimethyladenosine (mpU-m62A) and on the trinucleotide U-m62A-U. A detailed comparison is given of the conformational features of mpm62A-U and mpU-m62A with the corresponding 5'-nonphosphorylated dinucleotides m62A-U and U-m62A, respectively. The behaviour of the trinucleotide U-m62A-U is compared with the properties of the constituent dinucleotides U-m62A and mpm62A-U. Chemical-shift and CD data were used to determine the amount of stacking interactions. For each compound NMR spectra were recorded at two or three sample concentrations in order to separate intermolecular and intramolecular base-base interactions. The coupling constants of the ribose ring are interpreted in terms of the N/S equilibrium, and population distributions along the backbone angles beta, gamma and epsilon are presented. The combined data indicate a strong similarity between mpm62A-U and m62A-U both in degree and in mode of stacking. In contrast, the existence of different types of stacking interactions in mpU-m62A and U-m62A is suggested in order to explain the NMR and CD data. It is concluded that dinucleoside bisphosphates serve better as a model for the behaviour of trinucleotides than dinucleoside monophosphates. The trinucleotide U-m62A-U adopts a regular single-stranded stacked RNA structure with preference for N-type ribose and gamma+ and beta t backbone torsion angles. The difference in behaviour between the U-m62A- part of U-m62A-U and the dimer U-m62A is seen as a typical example of conformational transmission.
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24
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Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys 1987; 20:113-72. [PMID: 3327086 DOI: 10.1017/s0033583500004169] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).
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Affiliation(s)
- C Giessner-Prettre
- Laboratoire de Biochimie Théorique associé au C.N.R.S., Institut de Biologie Physico-Chimique, Paris, France
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Pathak T, Chattopadhyaya J. A regio and stereoselective synthesis of 2',2',3',4'-tetradeuterio-2'-deoxy nucleosides. Tetrahedron 1987. [DOI: 10.1016/s0040-4020(01)83465-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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