Abstract A five-dimensional (5D) APSY (automated projection spectroscopy) HCNCH experiment is presented, which allows unambiguous correlation of sugar to base nuclei in nucleic acids. The pulse sequence uses multiple quantum (MQ) evolution which enables long constant-time evolution periods in all dimensions, an improvement that can also benefit non-APSY applications. Applied with an RNA with 23 nucleotides the 5D APSY-HCNCH experiment produced a complete and highly precise 5D chemical shift list within 1.5 h. Alternatively, and for molecules where the out-and-stay 5D experiment sensitivity is not sufficient, a set of out-and-back 3D APSY-HCN experiments is proposed: an intra-base (3D APSY-b-HCN) experiment in an MQ or in a TROSY version, and an MQ sugar-to-base (3D APSY-s-HCN) experiment. The two 3D peak lists require subsequent matching via the N1/9 chemical shift values to one 5D peak list. Optimization of the 3D APSY experiments for maximal precision in the N1/9 dimension allowed matching of all 15N chemical shift values contained in both 3D peak lists. The precise 5D chemical shift correlation lists resulting from the 5D experiment or a pair of 3D experiments also provide a valuable basis for subsequent connection to chemical shifts derived with other experiments.
Content Type Journal Article
Category Article
Pages 1-10
DOI 10.1007/s10858-011-9588-z
Authors
Barbara Krähenbühl, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
Daniela Hofmann, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
Christophe Maris, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
Gerhard Wider, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
Measurement of 1Hâ??15N and 1Hâ??13C residual dipolar couplings in nucleic acids from TROSY intensities
Measurement of 1Hâ??15N and 1Hâ??13C residual dipolar couplings in nucleic acids from TROSY intensities
Abstract Analogous to the recently introduced ARTSY method for measurement of one-bond 1Hâ??15N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base 13Câ??1H and 15Nâ??1H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in 1Hâ??15N and 13Câ??1H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional...
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4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins
4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins
Abstract A four-dimensional (4D) APSY (automated projection spectroscopy)-HBCB(CG)CDHD experiment is presented. This 4D experiment correlates aromatic with aliphatic carbon and proton resonances from the same amino acid side chain of proteins in aqueous solution. It thus allows unambiguous sequence-specific assignment of aromatic amino acid ring signals based on backbone assignments. Compared to conventional 2D approaches, the inclusion of evolution periods on 1Hβ and 13Cδ...
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[NMR paper] Recommendations for the presentation of NMR structures of proteins and nucleic acids-
Recommendations for the presentation of NMR structures of proteins and nucleic acids--IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy.
Related Articles Recommendations for the presentation of NMR structures of proteins and nucleic acids--IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy.
Eur J Biochem. 1998 Aug 15;256(1):1-15
Authors: Markley JL, Bax A, Arata...
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[NMR paper] Recommendations for the presentation of NMR structures of proteins and nucleic acids.
Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.
Related Articles Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.
J Biomol NMR. 1998 Jul;12(1):1-23
Authors: Markley JL, Bax A, Arata Y,...
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[NMR paper] Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P N
Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P NMR.
Related Articles Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P NMR.
J Biochem. 1994 Feb;115(2):270-8
Authors: Odahara T, Nishimoto S, Katsutani N, Kyogoku Y, Morimoto Y, Matsushiro A, Akutsu H
The dynamic properties of nucleic acids in five different types of intact supramolecular systems, namely, chicken erythrocyte chromatin, the wild type and a deletion mutant of the lambda phage, lipid-containing phage PM2, and...
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08-22-2010 03:33 AM
[NMR paper] Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P N
Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P NMR.
Related Articles Dynamic properties of nucleic acids in biosupramolecular systems, as studied by 31P NMR.
J Biochem. 1994 Feb;115(2):270-8
Authors: Odahara T, Nishimoto S, Katsutani N, Kyogoku Y, Morimoto Y, Matsushiro A, Akutsu H
The dynamic properties of nucleic acids in five different types of intact supramolecular systems, namely, chicken erythrocyte chromatin, the wild type and a deletion mutant of the lambda phage, lipid-containing phage PM2, and...
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08-22-2010 03:33 AM
Use of chemical shifts for structural studies of nucleic acids
Use of chemical shifts for structural studies of nucleic acids
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 1 February 2010</br>
Sik Lok, Lam , Lai Man, Chi</br>
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Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments
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