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Todokoro Y, Miyasaka Y, Yagi H, Kainosho M, Fujiwara T, Akutsu H. Structural analysis of ATP bound to the F 1-ATPase β-subunit monomer by solid-state NMR- insight into the hydrolysis mechanism in F 1. Biophys Chem 2024; 309:107232. [PMID: 38593533 DOI: 10.1016/j.bpc.2024.107232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024]
Abstract
ATP-hydrolysis-associated conformational change of the β-subunit during the rotation of F1-ATPase (F1) has been discussed using cryo-electron microscopy (cryo-EM). Since it is worthwhile to further investigate the conformation of ATP at the catalytic subunit through an alternative approach, the structure of ATP bound to the F1β-subunit monomer (β) was analyzed by solid-state NMR. The adenosine conformation of ATP-β was similar to that of ATP analog in F1 crystal structures. 31P chemical shift analysis showed that the Pα and Pβ conformations of ATP-β are gauche-trans and trans-trans, respectively. The triphosphate chain is more extended in ATP-β than in ATP analog in F1 crystals. This appears to be in the state just before ATP hydrolysis. Furthermore, the ATP-β conformation is known to be more closed than the closed form in F1 crystal structures. In view of the cryo-EM results, ATP-β would be a model of the most closed β-subunit with ATP ready for hydrolysis in the hydrolysis stroke of the F1 rotation.
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Affiliation(s)
- Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan; Technical Support Division, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan.
| | - Yoshiyuki Miyasaka
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hiromasa Yagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Masatsune Kainosho
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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2
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Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R 1ρ relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2020; 74:457-471. [PMID: 32789613 PMCID: PMC7508749 DOI: 10.1007/s10858-020-00337-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/13/2020] [Indexed: 05/30/2023]
Abstract
NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson-Crick-like conformations. As Watson-Crick-like G·T mismatches have base pairing geometries similar to Watson-Crick base pairs, we hypothesized that they would mimic Watson-Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3' and C4' nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson-Crick conformation and that transitions toward tautomeric and anionic Watson-Crick-like G·T mismatches restore the canonical Watson-Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson-Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T-, and also establish sugar carbons as new non-exchangeable probes of this exchange process.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Nymirum, 4324 S. Alston Avenue, Durham, NC, 27713, USA
| | - Isaac Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Nymirum, 4324 S. Alston Avenue, Durham, NC, 27713, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Chemistry, Duke University, Durham, NC, 27710, USA.
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3
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Goldbourt A. Structural characterization of bacteriophage viruses by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:192-210. [PMID: 31779880 DOI: 10.1016/j.pnmrs.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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4
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Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
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5
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Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. JOURNAL OF BIOMOLECULAR NMR 2018; 70:229-244. [PMID: 29675775 PMCID: PMC6048961 DOI: 10.1007/s10858-018-0177-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
Abstract
NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1A-T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3' and C4' spin relaxation in the rotating frame (R1ρ) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1A-T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A-T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Mary C. Clay
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
| | - Hashim M. Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
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6
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Quinn CM, Lu M, Suiter CL, Hou G, Zhang H, Polenova T. Magic angle spinning NMR of viruses. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:21-40. [PMID: 25919197 PMCID: PMC4413014 DOI: 10.1016/j.pnmrs.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/02/2023]
Abstract
Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
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7
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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8
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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9
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Abramov G, Goldbourt A. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:219-230. [PMID: 24875850 DOI: 10.1007/s10858-014-9840-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 69978, Ramat Aviv, Tel Aviv, Israel
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10
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Morag O, Abramov G, Goldbourt A. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell. J Am Chem Soc 2014; 136:2292-301. [PMID: 24447194 DOI: 10.1021/ja412178n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Ramat Aviv 69978, Tel Aviv, Israel
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11
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Sergeyev IV, Day LA, Goldbourt A, McDermott AE. Chemical shifts for the unusual DNA structure in Pf1 bacteriophage from dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy. J Am Chem Soc 2011; 133:20208-17. [PMID: 21854063 DOI: 10.1021/ja2043062] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Solid-state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100 K, as well as non-DNP spectra at a variety of field strengths and at temperatures in the range 213-243 K, have allowed the assignment of the (13)C and (15)N resonances of the unusual DNA structure in the Pf1 virion. The (13)C chemical shifts of C3' and C5', considered to be key reporters of deoxyribose conformation, fall near or beyond the edges of their respective ranges in available databases. The (13)C and (15)N chemical shifts of the DNA bases have above-average values for AC4, AC5, CC5, TC2, and TC5, and below average values for AC8, GC8, and GN2, pointing to an absence of Watson-Crick hydrogen bonding, yet the presence of some type of aromatic ring interaction. Crosspeaks between Tyr40 of the coat protein and several DNA atoms suggest that Tyr40 is involved in this ring interaction. In addition, these crosspeak resonances and several deoxyribose resonances are multiply split, presumably through the effects of ordered but differing interactions between capsid protein subunits and each type of nucleotide in each of the two DNA strands. Overall, these observations characterize and support the DNA model proposed by Liu and Day and refined by Tsuboi et al., which calls for the most highly stretched and twisted naturally occurring DNA yet encountered.
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Affiliation(s)
- Ivan V Sergeyev
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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12
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Abramov G, Morag O, Goldbourt A. Magic-Angle Spinning NMR of a Class I Filamentous Bacteriophage Virus. J Phys Chem B 2011; 115:9671-80. [DOI: 10.1021/jp2040955] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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13
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Santini GPH, Cognet JAH, Xu D, Singarapu KK, Hervé du Penhoat C. Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC). J Phys Chem B 2009; 113:6881-93. [PMID: 19374420 DOI: 10.1021/jp8100656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Determination of DNA solution structure is a difficult task even with the high-sensitivity method used here based on simulated annealing with 35 restraints/residue (Cryoprobe 750 MHz NMR). The conformations of both the phosphodiester linkages and the dinucleotide segment encompassing the sharp turn in single-stranded DNA are often underdetermined. To obtain higher quality structures of a DNA GNRA loop, 5'-d(GCGAAAGC)-3', we have used a mesoscopic molecular modeling approach, called Biopolymer Chain Elasticity (BCE), to provide reference conformations. By construction, these models are the least deformed hairpin loop conformation derived from canonical B-DNA at the nucleotide level. We have further explored this molecular conformation at the torsion angle level with AMBER molecular mechanics using different possible (epsilon,zeta) constraints to interpret the 31P NMR data. This combined approach yields a more accurate molecular conformation, compatible with all the NMR data, than each method taken separately, NMR/DYANA or BCE/AMBER. In agreement with the principle of minimal deformation of the backbone, the hairpin motif is stabilized by maximal base-stacking interactions on both the 5'- and 3'-sides and by a sheared G.A mismatch base pair between the first and last loop nucleotides. The sharp turn is located between the third and fourth loop nucleotides, and only two torsion angles beta6 and gamma6 deviate strongly with respect to canonical B-DNA structure. Two other torsion angle pairs epsilon3,zeta3 and epsilon5,zeta5 exhibit the newly recognized stable conformation BIIzeta+ (-70 degrees, 140 degrees). This combined approach has proven to be useful for the interpretation of an unusual 31P chemical shift in the 5'-d(GCGAAAGC)-3' hairpin.
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Affiliation(s)
- Guillaume P H Santini
- Laboratoire de Biophysique Moleculaire, Cellulaire et Tissulaire, UMR 7033 CNRS, Universite Pierre et Marie Curie Paris 6, Genopole Campus 1, 5 rue Henri Desbrueres, Evry 91030, France
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14
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Ohlenschläger O, Haumann S, Ramachandran R, Görlach M. Conformational signatures of 13C chemical shifts in RNA ribose. JOURNAL OF BIOMOLECULAR NMR 2008; 42:139-42. [PMID: 18807198 DOI: 10.1007/s10858-008-9271-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Accepted: 08/18/2008] [Indexed: 05/13/2023]
Abstract
The conformational dependence of (13)C chemical shift values of RNA riboses determined by liquid-state NMR spectroscopy was evaluated using data deposited for RNA structures in the RCSD and BMRB data bases. Results derived support the applicability of the canonical coordinates approach of Rossi and Harbison (J Magn Reson 151:1-8, 2001) in liquid-state NMR to assess the sugar pucker of ribose units in RNA.
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Affiliation(s)
- Oliver Ohlenschläger
- Leibniz Institute for Age Research/Fritz Lipmann Institute, Biomolecular NMR Spectroscopy, Beutenbergstrasse 11, Jena, Germany.
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15
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Klumpp K, Kalayanov G, Ma H, Le Pogam S, Leveque V, Jiang WR, Inocencio N, De Witte A, Rajyaguru S, Tai E, Chanda S, Irwin MR, Sund C, Winqist A, Maltseva T, Eriksson S, Usova E, Smith M, Alker A, Najera I, Cammack N, Martin JA, Johansson NG, Smith DB. 2'-deoxy-4'-azido nucleoside analogs are highly potent inhibitors of hepatitis C virus replication despite the lack of 2'-alpha-hydroxyl groups. J Biol Chem 2007; 283:2167-75. [PMID: 18003608 DOI: 10.1074/jbc.m708929200] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerases effectively discriminate against deoxyribonucleotides and specifically recognize ribonucleotide substrates most likely through direct hydrogen bonding interaction with the 2'-alpha-hydroxy moieties of ribonucleosides. Therefore, ribonucleoside analogs as inhibitors of viral RNA polymerases have mostly been designed to retain hydrogen bonding potential at this site for optimal inhibitory potency. Here, two novel nucleoside triphosphate analogs are described, which are efficiently incorporated into nascent RNA by the RNA-dependent RNA polymerase NS5B of hepatitis C virus (HCV), causing chain termination, despite the lack of alpha-hydroxy moieties. 2'-deoxy-2'-beta-fluoro-4'-azidocytidine (RO-0622) and 2'-deoxy-2'-beta-hydroxy-4'-azidocytidine (RO-9187) were excellent substrates for deoxycytidine kinase and were phosphorylated with efficiencies up to 3-fold higher than deoxycytidine. As compared with previous reports on ribonucleosides, higher levels of triphosphate were formed from RO-9187 in primary human hepatocytes, and both compounds were potent inhibitors of HCV virus replication in the replicon system (IC(50) = 171 +/- 12 nM and 24 +/- 3 nM for RO-9187 and RO-0622, respectively; CC(50) >1 mM for both). Both compounds inhibited RNA synthesis by HCV polymerases from either HCV genotypes 1a and 1b or containing S96T or S282T point mutations with similar potencies, suggesting no cross-resistance with either R1479 (4'-azidocytidine) or 2'-C-methyl nucleosides. Pharmacokinetic studies with RO-9187 in rats and dogs showed that plasma concentrations exceeding HCV replicon IC(50) values 8-150-fold could be achieved by low dose (10 mg/kg) oral administration. Therefore, 2'-alpha-deoxy-4'-azido nucleosides are a new class of antiviral nucleosides with promising preclinical properties as potential medicines for the treatment of HCV infection.
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Affiliation(s)
- Klaus Klumpp
- Roche Palo Alto LLC, Palo Alto, California 94304, USA.
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16
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Matsugami A, Xu Y, Noguchi Y, Sugiyama H, Katahira M. Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+
solution. FEBS J 2007; 274:3545-3556. [PMID: 17561958 DOI: 10.1111/j.1742-4658.2007.05881.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of human telomeric DNA is controversial; it depends upon the sequence contexts and the methodologies used to determine it. The solution structure in the presence of K(+) is particularly interesting, but the structure is yet to be elucidated, due to possible conformational heterogeneity. Here, a unique strategy is applied to stabilize one such structure in a K(+) solution by substituting guanosines with 8-bromoguanosines at proper positions. The resulting spectra are cleaner and led to determination of the structure at a high atomic resolution. This demonstrates that the application of 8-bromoguanosine is a powerful tool to overcome the difficulty of nucleic acid structure determination arising from conformational heterogeneity. The obtained structure is a mixed-parallel/antiparallel quadruplex. The structure of telomeric DNA was recently reported in another study, in which stabilization was brought about by mutation and resultant additional interactions [Luu KN, Phan AT, Kuryavyi V, Lacroix L & Patel DJ (2006) Structure of the human telomere in K(+) solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128, 9963-9970]. The structure of the guanine tracts was similar between the two. However, a difference was seen for loops connecting guanine tracts, which may play a role in the higher order arrangement of telomeres. Our structure can be utilized to design a small molecule which stabilizes the quadruplex. This type of molecule is supposed to inhibit a telomerase and thus is expected to be a candidate anticancer drug.
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Affiliation(s)
- Akimasa Matsugami
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Yan Xu
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Yuuki Noguchi
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Hiroshi Sugiyama
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Masato Katahira
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
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17
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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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18
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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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19
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Leal C, Topgaard D, Martin RW, Wennerström H. NMR Studies of Molecular Mobility in a DNA−Amphiphile Complex. J Phys Chem B 2004. [DOI: 10.1021/jp0480495] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cecília Leal
- Physical Chemistry1, Lund University, POB 124, 221 00 Lund, Sweden and Materials Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, California 94720
| | - Daniel Topgaard
- Physical Chemistry1, Lund University, POB 124, 221 00 Lund, Sweden and Materials Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, California 94720
| | - Rachel W. Martin
- Physical Chemistry1, Lund University, POB 124, 221 00 Lund, Sweden and Materials Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, California 94720
| | - Håkan Wennerström
- Physical Chemistry1, Lund University, POB 124, 221 00 Lund, Sweden and Materials Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, California 94720
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20
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Kwok CW, Ho CN, Chi LM, Lam SL. Random coil carbon chemical shifts of deoxyribonucleic acids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 166:11-18. [PMID: 14675814 DOI: 10.1016/j.jmr.2003.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The sequence and temperature effects on random coil DNA carbon chemical shifts have been investigated using sixteen 17-nucleotide sequences. Temperature effect correction parameters have been determined for the aromatic C6/C8 carbons and the deoxyribose C1', C2', and C3' carbons. The carbon chemical shifts of a specific nucleotide in a random coil sequence have been shown to depend mainly on the type of its nearest neighbors. A carbon chemical shift database containing all 64 different types of triplets has been established for predicting random coil DNA carbon chemical shifts. The use of this triplet database for carbon chemical shift predictions shows good accuracy with experimental data, with root-mean-square deviations of 0.09, 0.10, 0.10, and 0.10 ppm and correlation coefficients of 0.999, 0.996, 0.978, and 0.974 for C6/C8, C1', C2', and C3', respectively.
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Affiliation(s)
- Chit Wan Kwok
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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21
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Matsugami A, Okuizumi T, Uesugi S, Katahira M. Intramolecular higher order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA. J Biol Chem 2003; 278:28147-53. [PMID: 12748183 DOI: 10.1074/jbc.m303694200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GGA triplet repeats are widely dispersed throughout eukaryotic genomes and are frequently located within biologically important regions such as gene regulatory regions and recombination hot spot sites. We determined the structure of d(GGA)4 (12-mer) under physiological conditions and founded the formation of an intramolecular parallel quadruplex for the first time. Later, a similar architecture to that of the intramolecular parallel quadruplex was found for a telomere DNA in the crystalline state. Here, we have determined the structure of d(GGA)8 (24-mer) under physiological conditions. Two intramolecular parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad are formed in d(GGA)8. These quadruplexes are packed in a tail-to-tail manner. This is the first demonstration of the intramolecular higher order packing of quadruplexes at atomic resolution. K+ ions, but not Na+ ones, are critically required for the formation of this unique structure. The elucidated structure suggests the mechanisms underlying the biological events related to the GGA triplet repeat. Furthermore, in the light of the structure, the mode of the higher order packing of the telomere DNA is discussed.
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Affiliation(s)
- Akimasa Matsugami
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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22
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van Dam L, Ouwerkerk N, Brinkmann A, Raap J, Levitt MH. Solid-state NMR determination of sugar ring pucker in (13)C-labeled 2'-deoxynucleosides. Biophys J 2002; 83:2835-44. [PMID: 12414715 PMCID: PMC1302367 DOI: 10.1016/s0006-3495(02)75292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The H3'-C3'-C4'-H4' torsional angles of two microcrystalline 2'-deoxynucleosides, thymidine and 2'-deoxycytidine.HCl, doubly (13)C-labeled at the C3' and C4' positions of the sugar ring, have been measured by solid-state magic-angle-spinning nuclear magnetic resonance (NMR). A double-quantum heteronuclear local field experiment with frequency-switched Lee-Goldberg homonuclear decoupling was used. The H3'-C3'-C4'-H4' torsional angles were obtained by comparing the experimental curves with numerical simulations, including the two (13)C nuclei, the directly bonded (1)H nuclei, and five remote protons. The H3'-C3'-C4'-H4' angles were converted into sugar pucker angles and compared with crystallographic data. The delta torsional angles determined by solid-state NMR and x-ray crystallography agree within experimental error. Evidence is also obtained that the proton positions may be unreliable in the x-ray structures. This work confirms that double-quantum solid-state NMR is a feasible tool for studying sugar pucker conformations in macromolecular complexes that are unsuitable for solution NMR or crystallography.
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Affiliation(s)
- Lorens van Dam
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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23
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Matsugami A, Ouhashi K, Kanagawa M, Liu H, Kanagawa S, Uesugi S, Katahira M. An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction. J Mol Biol 2001; 313:255-69. [PMID: 11800555 DOI: 10.1006/jmbi.2001.5047] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K(+) conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.
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Affiliation(s)
- A Matsugami
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
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24
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Rossi P, Harbison GS. Calculation of 13C chemical shifts in rna nucleosides: structure-13C chemical shift relationships. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 151:1-8. [PMID: 11444931 DOI: 10.1006/jmre.2001.2350] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Isotropic 13C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting 13C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average of 5 ppm while the GIAO-SCF underestimates the shifts by the same amount. However, in the majority of cases the errors appear to be systematic, as the slope of a plot of calculated vs experimental shifts is very close to unity, with minimal scatter. The values of the 13C NMR shifts of the ribose sugar are therefore sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.
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Affiliation(s)
- P Rossi
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, Nebraska 68588-0304, USA
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25
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Ebrahimi M, Rossi P, Rogers C, Harbison GS. Dependence of 13C NMR chemical shifts on conformations of rna nucleosides and nucleotides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 150:1-9. [PMID: 11330976 DOI: 10.1006/jmre.2001.2314] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Cross-polarization magic-angle spinning solid-state NMR spectroscopy has been used to investigate the dependence of (13)C sugar chemical shifts on specific conformational parameters of a variety of ribonucleotides and ribonucleosides. Solid-state NMR is a valuable tool for nucleoside and nucleotide structural studies since it provides the means to acquire spectra that correspond to single conformations, as opposed to (13)C solution NMR methods. The distinct effects of sugar puckering on the C1', C4', and C5' resonances of C2' endo (S type) and C3' endo (N type) furanoid conformations allow us to separate them into two groups. Further analysis of each group reveals an additional dependence of the C1' and C5' resonances on the glycosidic and C4'-C5' exocyclic torsion angles, respectively. However, it is found that the glycosidic conformation cannot independently be determined from sugar (13)C chemical shift data. The statistical methods of exploratory data analysis and discriminant analysis are used to construct two canonical coordinates-linear combinations of chemical shifts which give the statistically optimal determination of the conformation from the NMR data.
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Affiliation(s)
- M Ebrahimi
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, Nebraska 68588-0304, USA
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26
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Metzler DE, Metzler CM, Sauke DJ. The Nucleic Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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van Dam L, Levitt MH. BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA. J Mol Biol 2000; 304:541-61. [PMID: 11099379 DOI: 10.1006/jmbi.2000.4194] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A combination of solid-state (31)P and (13)C NMR, X-ray diffraction, and model building is used to show that the B and C forms of fibrous macromolecular DNA consist of two distinct nucleotide conformations, which correspond closely to the BI and BII nucleotide conformations known from oligonucleotide crystals. The proportion of the BII conformation is higher in the C form than in the B form. We show structural models for a 10(1) double helix involving BI nucleotides and a 9(1) double helix involving BII nucleotides. The 10(1) BI model is similar to a previous model of B-form DNA, while the 9(1) BII model is novel. The BII model has a very deep and narrow minor groove, a shallow and wide major groove, and highly inclined bases. This work shows that the B to C transition in fibers corresponds to BI to BII conformational changes of the individual nucleotides.
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Affiliation(s)
- L van Dam
- Department of Physical Chemistry Arrhenius Laboratory, Stockholm University, Stockholm, S-106 91, Sweden.
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28
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Xu XP, Au−Yeung SCF. Investigation of Chemical Shift and Structure Relationships in Nucleic Acids Using NMR and Density Functional Theory Methods. J Phys Chem B 2000. [DOI: 10.1021/jp0007538] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao-Ping Xu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Steve C. F. Au−Yeung
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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29
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Kiihne SR, Geahigan KB, Oyler NA, Zebroski H, Mehta MA, Drobny GP. Distance Measurements in Multiply Labeled Crystalline Cytidines by Dipolar Recoupling Solid State NMR. J Phys Chem A 1999. [DOI: 10.1021/jp990719x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. R. Kiihne
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
| | - K. B. Geahigan
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
| | - N. A. Oyler
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
| | - H. Zebroski
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
| | - M. A. Mehta
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
| | - G. P. Drobny
- Departments of Chemistry and Physics, University of Washington, Seattle, Washington 98195
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30
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Kojima C, Ono A, Kainosho M, James TL. DNA duplex dynamics: NMR relaxation studies of a decamer with uniformly 13C-labeled purine nucleotides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 135:310-333. [PMID: 9878461 DOI: 10.1006/jmre.1998.1584] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dynamics in a DNA decamer duplex, d(CATTTGCATC). d(GATGCAAATG), were investigated via a detailed 13C NMR relaxation study. Every 2'-deoxyadenosine and 2'-deoxyguanidine was chemically enriched with 15% 13C and 98% 15N isotopes. Six nuclear relaxation parameters [R(13Cz), R(1Hz), R(2(1)Hz13Cz), R(13Cx), R(2(1)Hz13Cx) and steady-state 13C¿1H¿ NOE] were measured at 600 MHz and three were measured at 500 MHz (1H frequency) for the CH spin systems of sugar 1', 3', and 4' as well as base 8 and 2 positions. A dependence of relaxation parameter values on chemical position was clearly observed; however, no sequence-specific variation was readily evident within our experimental error of approximately 5-10%, except for 3' and 5' termini. It was demonstrated that the random 15% 13C enrichment effectively suppressed both scalar and dipolar contributions of the neighboring carbons and protons on the relaxation parameters. To analyze dynamics via all observed relaxation parameters, full spectral density mapping (1992, J. W. Peng and G. Wagner, J. Magn. Reson. 98, 308) and the "model-free" approach (1982, Lipari and Szabo, J. Am. Chem. Soc. 104, 4546) were applied complementarily. A linear correlation between three spectral density values, J(omegaC), J(omegaH - omegaC), and J(omegaH + omegaC) was observed in plots containing all measured values, but not for the other spectral density terms including J(0). These linear correlations reflect the effect of overall motion and similar internal motions for each CH vector in the decamer. The correlations yielded two correlation times, 3-4 ns and 10-200 ps. One value, 3-4 ns, corresponds to the value of 3.3 ns obtained for the overall isotropic tumbling correlation time determined from analysis of 13C T1/T2 ratios. The possibility of overall anisotropic tumbling was examined, but statistical analysis showed no advantage over the assumption of simple isotropic tumbling. Lack of correlations entailing J(0) implies that a relatively slow chemical exchange contributes to yielding of effective Jeff(0) values. Based on spectral density mapping and the T1/T2 ratio analysis, three basic assumptions were initially employed (and subsequently justified) for the model-free calculation: isotropic overall tumbling, one internal motion, and the presence of chemical exchange terms. Except for terminal residues, the order parameter S2 and the corresponding fast internal motion correlation time were determined to be about 0.8 +/- 0.1 and 20 +/- 20 ps, respectively, for the various CH vectors. Only a few differences were observed between or within sugars and bases. The internal motion is very fast (ps-ns time scale) and its amplitude restricted; e.g., assuming a simple wobble-in-a-cone model, the internal motion is restricted to an angular amplitude of +/-22. 5 degrees for each of the 1', 3', 4', 2, and 8 positions in the purine nucleotides in the entire duplex.
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Affiliation(s)
- C Kojima
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143-0446, USA
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31
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Case DA. The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 1998; 8:624-30. [PMID: 9818268 DOI: 10.1016/s0959-440x(98)80155-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The existence of chemical shift dispersion is crucial for the application of NMR spectroscopy to biomolecules, but the direct interpretation of shift tensors in terms of structure and dynamics is often difficult. Proton shifts reflect environmental influences from nearby aromatic groups, metal sites or hydrogen-bonding partners. These effects can be reasonably modeled with empirical equations, but multiple contributions to shifts can be difficult to disentangle. Shifts for carbon and nitrogen generally reflect local bonding interactions, often in ways that allow the local structure to be inferred. The anisotropy of the shielding tensor is also of interest. It influences the resonance position in partially-ordered samples and has consequences for spin relaxation, even in isotropic systems. There has been recent progress in measuring and interpreting these anisotropies.
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Affiliation(s)
- D A Case
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
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32
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Kalurachchi K, Nikonowicz EP. NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA. J Mol Biol 1998; 280:639-54. [PMID: 9677294 DOI: 10.1006/jmbi.1998.1915] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many cellular processes involve the preferential interaction of an RNA molecule with a specific protein. A detailed analysis of the individual protein and RNA components of these interactions can provide unique insights into the structural features important for protein-RNA recognition. Ribosomal protein S8 of Escherichia coli plays a key role in 30 S ribosomal subunit assembly through its interaction with 16 S rRNA. The binding site for protein S8 comprises a portion of helix 21, nucleotides G588 to G604 and C634 to C651. This region forms a base-paired helix that is interrupted by a non-Watson-Crick segment composed of nine phylogenetically conserved nucleotides. We have investigated the detailed structure of the conserved segment and the interaction of this region with metal ions using NMR spectroscopy. Twenty-four of the 40 calculated structures converged to similar conformations and were grouped into two families. The main difference between the families is the orientation of the base of U641. The rms deviation between the heavy-atoms of the ten lowest-energy structures is 1.24 A. The orientations of the G597.C643 base-pair and A595.(A596.U644) base-triple within the conserved core have been defined and appear to extend the proximal segment of helix 21 into the phylogenetically conserved core. The base of A642 terminates this helix by stacking against C643 and the base of U641 forms hydrogen bonds with core nucleotides. The conserved core also contains a Mg2+-binding site that promotes stabilization of the secondary and tertiary structure elements of the core. A model for the interaction of S8 with its RNA-binding site is proposed.
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Affiliation(s)
- K Kalurachchi
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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33
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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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Xu XP, Chiu WLAK, Au-Yeung SCF. Chemical Shift and Structure Relationship in Nucleic Acids: Correlation of Backbone Torsion Angles γ and α with 13C Chemical Shifts. J Am Chem Soc 1998. [DOI: 10.1021/ja972607u] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiao-Ping Xu
- Department of Chemistry The Chinese University of Hong Kong Shatin, New Territories, Hong Kong
| | - Wing-Lok A. K. Chiu
- Department of Chemistry The Chinese University of Hong Kong Shatin, New Territories, Hong Kong
| | - Steve C. F. Au-Yeung
- Department of Chemistry The Chinese University of Hong Kong Shatin, New Territories, Hong Kong
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35
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Abstract
The application of high-resolution, multidimensional NMR techniques to the problem of determining the structure of drug-DNA complexes in solution has led to substantial progress in understanding the effect of drugs on DNA at the molecular level. With the development of isotopic labeling methods applied in three- and four-dimensional experiments, we anticipate that more complex drug-DNA systems will become amenable to structural analysis. In addition to implementing these newer techniques, progress will also be made in terms of investigating the structure of drug complexes with more unusual forms of DNA, such as triplexes, quadruplexes, multistranded junctions, and so forth.
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Affiliation(s)
- M A Keniry
- Research School of Chemistry, Australian National University, Canberra, Australia
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Affiliation(s)
- C L Juang
- Academia Sinica, Nankang, Republic of China
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37
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Carlström G, Chen SM, Miick S, Chazin WJ. NMR studies of complex DNA structures: the Holliday junction intermediate in genetic recombination. Methods Enzymol 1995; 261:163-82. [PMID: 8569494 DOI: 10.1016/s0076-6879(95)61009-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- G Carlström
- Department of Physical Chemistry, Lund University, Sweden
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38
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Schmieder P, Ippel JH, van den Elst H, van der Marel GA, van Boom JH, Altona C, Kessler H. Heteronuclear NMR of DNA with the heteronucleus in natural abundance: facilitated assignment and extraction of coupling constants. Nucleic Acids Res 1992; 20:4747-51. [PMID: 1408787 PMCID: PMC334227 DOI: 10.1093/nar/20.18.4747] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Two heteronuclear proton-carbon NMR experiments are applied to the DNA-octamer d(TTGGCCAA)2 with carbon in natural abundance. They lead to a complete assignment of the carbon resonances of the sugars and bases. In addition, several heteronuclear coupling constants, proton-carbon as well as proton-phosphorous and phosphorous-carbon, were determined. The information can be obtained in a reasonable measuring time and offers valuable information for a detailed picture of DNA structure.
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Affiliation(s)
- P Schmieder
- Organisch-Chemisches Institut, TU München, Garching, Germany
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Tang P, Juang CL, Harbison GS. Intercalation complex of proflavine with DNA: structure and dynamics by solid-state NMR. Science 1990; 249:70-2. [PMID: 2367853 DOI: 10.1126/science.2367853] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallel to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.
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Affiliation(s)
- P Tang
- Department of Chemistry, State University of New York, Stony Brook 11794-3400
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