1
|
Baranowski D, Mieczkowski A, Trzybiński D, Woźniak K, Bednarska-Szczepaniak K, Gdaniec Z, Leśnikowski ZJ. INSIGHTS INTO MOLECULAR STRUCTURE OF ADENOSINE-BORON CLUSTER CONJUGATES AND THEIRS PHENYL ISOSTERS AS ADENOSINE RECEPTOR LIGANDS: NUCLEAR MAGNETIC RESONANCE, CRYSTALLOGRAPHIC AND COMPUTATIONAL STUDIES. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
2
|
Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
Collapse
Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
3
|
Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, Trantírek L. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:53-62. [PMID: 26685997 PMCID: PMC4742510 DOI: 10.1007/s10858-015-0005-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
Collapse
Affiliation(s)
- Andrea Vavrinská
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiří Zelinka
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
| |
Collapse
|
4
|
Fonville JM, Swart M, Vokáčová Z, Sychrovský V, Šponer JE, Šponer J, Hilbers CW, Bickelhaupt FM, Wijmenga SS. Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Chemistry 2012; 18:12372-87. [PMID: 22899588 DOI: 10.1002/chem.201103593] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/10/2022]
Abstract
NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1)H and (13)C NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13)C and (1)H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.
Collapse
Affiliation(s)
- Judith M Fonville
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Sychrovský V, Sochorová Vokáčová Z, Trantírek L. Guanine bases in DNA G-quadruplex adopt nonplanar geometries owing to solvation and base pairing. J Phys Chem A 2012; 116:4144-51. [PMID: 22471881 DOI: 10.1021/jp2110049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The effect of base pairing and solvation on pyramidalization of the glycosidic nitrogen found in the residues of parallel G-quadruplex with NDB ID UDF062 is analyzed and explained with theoretical calculations. The extent of the pyramidalization depends on the local geometry of the 2'-deoxyguanosine residues, namely on their glycosidic torsion and sugar pucker, which are predetermined by the 3D-architecture of G-quadruplex. Pyramidal inversion of the glycosidic nitrogen found in 2'-deoxyguanosines of G-quadruplex is induced owing to site-specifically coordinated solvent. Different adiabatic structural constraints used for fixing the base-to-sugar orientation of 2'-deoxyguanosine in geometry optimizations result in different extents of pyramidalization and induce pyramidal inversion of the glycosidic nitrogen. These model geometry constraints helped us analyze the effect of real constraints represented by explicit molecular environment of selected residues of the G-quadruplex. The maximal extent of the glycosidic nitrogen pyramidalization found in the high-resolution crystal structure corresponds to the calculation to deformation energy of only 1 kcal mol(-1). The out-of-plane deformations of nucleobases thus provide a way for compensating the site-specific external environmental stress on the G-quadruplex.
Collapse
Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic.
| | | | | |
Collapse
|
6
|
Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, Pasulka J, Hofr C, Vanacova S, Stefl R. Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein. J Biol Chem 2010; 286:3645-57. [PMID: 21084293 PMCID: PMC3030368 DOI: 10.1074/jbc.m110.158774] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Non-coding RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex. The Nrd1 complex includes two RNA-binding proteins, the nuclear polyadenylated RNA-binding (Nab) 3 and the nuclear pre-mRNA down-regulation (Nrd) 1 that bind their specific termination elements. Here we report the solution structure of the RNA-recognition motif (RRM) of Nab3 in complex with a UCUU oligonucleotide, representing the Nab3 termination element. The structure shows that the first three nucleotides of UCUU are accommodated on the β-sheet surface of Nab3 RRM, but reveals a sequence-specific recognition only for the central cytidine and uridine. The specific contacts we identified are important for binding affinity in vitro as well as for yeast viability. Furthermore, we show that both RNA-binding motifs of Nab3 and Nrd1 alone bind their termination elements with a weak affinity. Interestingly, when Nab3 and Nrd1 form a heterodimer, the affinity to RNA is significantly increased due to the cooperative binding. These findings are in accordance with the model of their function in the poly(A) independent termination, in which binding to the combined and/or repetitive termination elements elicits efficient termination.
Collapse
Affiliation(s)
- Fruzsina Hobor
- National Centre for Biomolecular Research, Central European Institute of Technology, Faculty of Science, Masaryk University, Brno CZ-62500, Czechia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Vokáčová Z, Trantírek L, Sychrovský V. Evaluating the Effects of the Nonplanarity of Nucleic Acid Bases on NMR, IR, and Vibrational Circular Dichroism Spectra: A Density Functional Theory Computational Study. J Phys Chem A 2010; 114:10202-8. [DOI: 10.1021/jp102329t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zuzana Vokáčová
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic, and Biology Centre, v.v.i., Academy of Sciences of the Czech Republic, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Lukáš Trantírek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic, and Biology Centre, v.v.i., Academy of Sciences of the Czech Republic, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic, and Biology Centre, v.v.i., Academy of Sciences of the Czech Republic, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| |
Collapse
|
8
|
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1573-80. [PMID: 20559630 PMCID: PMC2975913 DOI: 10.1007/s00249-010-0614-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 11/20/2022]
Abstract
The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants 3J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution.
Collapse
|
9
|
Sychrovsky V, Foldynova-Trantirkova S, Spackova N, Robeyns K, Van Meervelt L, Blankenfeldt W, Vokacova Z, Sponer J, Trantirek L. Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion. Nucleic Acids Res 2010; 37:7321-31. [PMID: 19786496 PMCID: PMC2790901 DOI: 10.1093/nar/gkp783] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.
Collapse
Affiliation(s)
- Vladimir Sychrovsky
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo namesti 2, CZ, 16610 Prague, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Hritz J, Oostenbrink C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. J Phys Chem B 2009; 113:12711-20. [PMID: 19722597 DOI: 10.1021/jp902968m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such compounds. We present an enhanced sampling-one step perturbation method (ES-OS) to tackle this problem in a highly efficient way. A single molecular dynamics simulation of a judiciously chosen reference state (using two sets of soft-core interactions) is sufficient to determine conformational distributions of chemically similar compounds and the free energy differences between them. The ES-OS method is applied to a set of five biologically relevant 8-substituted GTP analogs having high energy barriers between the anti and the syn conformations of the base with respect to the ribose part. The reliability of ES-OS is verified by comparing the results to Hamiltonian replica exchange simulations of GTP and 8-Br-GTP and the experimentally determined 3J(C4,H1') coupling constant for GMP in water. Additional simulations in vacuum and octanol allow us to calculate differences in the solvation free energies and in lipophilicities (log P). Free energy contributions from individual conformational regions are also calculated, and their relationship with the overall free energy is derived leading to a set of multiconformational free energy formulas. These relationships are of general applicability and can be used in free energy calculations for a more diverse set of compounds.
Collapse
Affiliation(s)
- Jozef Hritz
- Leiden Amsterdam Center for Drug Research, Division of Molecular Toxicology, VU University Amsterdam, The Netherlands
| | | |
Collapse
|
11
|
Vokáčová Z, Bickelhaupt FM, Šponer J, Sychrovský V. Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing. J Phys Chem A 2009; 113:8379-86. [DOI: 10.1021/jp902473v] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zuzana Vokáčová
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - F. Matthias Bickelhaupt
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - JiYí Šponer
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
12
|
Webba da Silva M. NMR methods for studying quadruplex nucleic acids. Methods 2008; 43:264-77. [PMID: 17967697 DOI: 10.1016/j.ymeth.2007.05.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 05/16/2007] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.
Collapse
Affiliation(s)
- Mateus Webba da Silva
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine BT52 1SA, UK.
| |
Collapse
|
13
|
Abstract
This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.
Collapse
|
14
|
Rinnenthal J, Richter C, Ferner J, Duchardt E, Schwalbe H. Quantitative gamma-HCNCH: determination of the glycosidic torsion angle chi in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2007; 39:17-29. [PMID: 17641824 DOI: 10.1007/s10858-007-9167-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/22/2007] [Accepted: 05/22/2007] [Indexed: 05/16/2023]
Abstract
A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides. The quantitative Gamma-HCNCH measures the dipolar cross-correlated relaxation rates Gamma(DD,DD)(C8H8,C1'H1') (pyrimidines) and Gamma(DD,DD)(C6H6,C1'H1') (purines). Cross-correlated relaxation rates of a (13)C,(15)N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded chi-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the chi-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.
Collapse
Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | | | | | | | | |
Collapse
|
15
|
Affiliation(s)
- Mark Lukin
- Department of Pharmacological Sciences, State University of New York at Stony Brook, School of Medicine, 11794-8651, USA
| | | |
Collapse
|
16
|
Ihle Y, Ohlenschläger O, Häfner S, Duchardt E, Zacharias M, Seitz S, Zell R, Ramachandran R, Görlach M. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA. Nucleic Acids Res 2005; 33:2003-11. [PMID: 15814817 PMCID: PMC1074726 DOI: 10.1093/nar/gki501] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/07/2005] [Accepted: 03/21/2005] [Indexed: 11/24/2022] Open
Abstract
The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.
Collapse
Affiliation(s)
- Yvonne Ihle
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Sabine Häfner
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Elke Duchardt
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
| | - Martin Zacharias
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
| | - Simone Seitz
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Roland Zell
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Ramadurai Ramachandran
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Matthias Görlach
- To whom correspondence should be addressed. Tel: +49 3641 656220; Fax: +49 3641 656225;
| |
Collapse
|
17
|
Abstract
NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
Collapse
Affiliation(s)
- Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
18
|
Duchardt E, Richter C, Ohlenschläger O, Görlach M, Wöhnert J, Schwalbe H. Determination of the glycosidic bond angle chi in RNA from cross-correlated relaxation of CH dipolar coupling and N chemical shift anisotropy. J Am Chem Soc 2004; 126:1962-70. [PMID: 14971929 DOI: 10.1021/ja0367041] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new heteronuclear NMR pulse sequence, the quantitative Gamma(HCN) experiment, for the determination of the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides is described. The Gamma(HCN) experiment allows measurement of CH dipole-dipole, N chemical shift anisotropy cross-correlated relaxation rates (Gamma(C1'H1',N1)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for pyrimidines Gamma(C1'H1'N9)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for purines). A nucleotide-specific parametrization for the dependence of these Gamma-rates on chi based on (15)N chemical shift tensors determined by solid-state NMR experiments on mononucleosides (Stueber, D.; Grant, D. M. J. Am. Chem. Soc. 2002, 124, 10539-10551) is presented. For a 14-mer and a 30-mer RNA of known structures, it is found that the Gamma(HCN) experiment offers a very sensitive parameter for changes in the angle chi and allows restraining of chi with an accuracy of around 10 degrees for residues which do not undergo conformational averaging. Therefore, the Gamma(HCN) experiment can be used for the determination of chi in addition to data derived from (3)J(C,H)-coupling constants. As shown for the 30-mer RNA, the derived torsion angle information can be incorporated as additional restraint, improving RNA structure calculations.
Collapse
Affiliation(s)
- Elke Duchardt
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Marie-Curie-Strasse 11, D-60439 Frankfurt/Main, Germany
| | | | | | | | | | | |
Collapse
|
19
|
Stefl R, Wu H, Ravindranathan S, Sklenár V, Feigon J. DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum. Proc Natl Acad Sci U S A 2004; 101:1177-82. [PMID: 14739342 PMCID: PMC337026 DOI: 10.1073/pnas.0308143100] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.
Collapse
Affiliation(s)
- Richard Stefl
- National Center for Biomolecular Research, NMR Laboratory, Faculty of Science, Masaryk University, Kotlárská 2, CZ-611 37 Brno, Czech Republic
| | | | | | | | | |
Collapse
|
20
|
Munzarová ML, Sklenár V. DFT analysis of NMR scalar interactions across the glycosidic bond in DNA. J Am Chem Soc 2003; 125:3649-58. [PMID: 12643728 DOI: 10.1021/ja028931t] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relationship between the glycosidic torsion angle chi, the three-bond couplings (3)J(C2/4-H1') and (3)J(C6/8-H1'), and the one-bond coupling (1)J(C1'-H1') in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and chi depend strongly on the aromatic base. (3)J(C2/4-H1') reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of (3)J(C6/8-H1'), an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10 degrees with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases (3)J(C2/4-H1') and (3)J(C6/8-H1'), while increasing (1)J(C1'-H1') for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on (1)J(C1'-H1') is interpreted in terms of interactions between the n(O4'), sigma*(C1'-H1') orbitals. The (1)J(C1'-H1') are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos(2)(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical (3)J(C2/4-H1') and (3)J(C6/8-H1') for uracil cyclo-nucleosides compare well with available experimental data. (3)J(C6/8-H1') couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a nonlocal aspect of the spin-spin interactions across the glycosidic bond. Theoretical (1)J(C1'-H1') are underestimated with respect to the experiment by ca. 10% but reproduce the trends in (1)J(C1'-H1') vs chi.
Collapse
Affiliation(s)
- Markéta L Munzarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, CZ-611 37 Brno, Czech Republic.
| | | |
Collapse
|
21
|
Munzarová ML, Sklenár V. Three-bond sugar-base couplings in purine versus pyrimidine nucleosides: a DFT study of Karplus relationships for (3)J(C2/4-H1') and (3)J(C6/8-H1') in DNA. J Am Chem Soc 2002; 124:10666-7. [PMID: 12207516 DOI: 10.1021/ja026502p] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(3)J(C2/4-H1') and (3)J(C6/8-H1') scalar spin-spin coupling constants have been calculated for deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine as functions of the glycosidic torsion angle chi by means of density functional theory. Except for deoxythymidine, (3)J(C2/4-H1') depends little on the base type. On the contrary, (3)J(C6/8-H1') follows the usual trans to cis ratio ((3)J(C-H(cis)) < (3)J(C-H(trans))) for purine nucleosides, but reveals the opposite relation ((3)J(C-H(cis)) > (3)J(C-H(trans))) for pyrimidine nucleosides. Our results compare well with the experiment for deoxyguanosine and predict a novel trend in the case of pyrimidine bases for which no NMR results are available in the syn region. A breakdown of the key Fermi contact part of (3)J(C6/8-H1') into MO contributions rationalizes this trend in terms of an unusual coupling mechanism in the syn orientation that is very effective for pyrimidine nucleosides and considerably weaker for purine nucleosides.
Collapse
Affiliation(s)
- Markéta L Munzarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, CZ-611 37 Brno, Czech Republic.
| | | |
Collapse
|