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Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. Biochemistry 2019; 58:1963-1974. [PMID: 30950607 DOI: 10.1021/acs.biochem.9b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A( syn)-T and G( syn)-C+ Hoogsteen base pairs in protein-bound DNA duplexes can be difficult to resolve by X-ray crystallography due to ambiguous electron density and by nuclear magnetic resonance (NMR) spectroscopy due to poor chemical shift dispersion and size limitations with solution-state NMR spectroscopy. Here we describe an NMR strategy for characterizing Hoogsteen base pairs in protein-DNA complexes, which relies on site-specifically incorporating 13C- and 15N-labeled nucleotides into DNA duplexes for unambiguous resonance assignment and to improve spectral resolution. The approach was used to resolve the conformation of an A-T base pair in a crystal structure of an ∼43 kDa complex between a 34 bp duplex DNA and the integration host factor (IHF) protein. In the crystal structure (Protein Data Bank entry 1IHF ), this base pair adopts an unusual Hoogsteen conformation with a distorted sugar backbone that is accommodated by a nearby nick used to aid in crystallization. The NMR chemical shifts and interproton nuclear Overhauser effects indicate that this base pair predominantly adopts a Watson-Crick conformation in the intact DNA-IHF complex under solution conditions. Consistent with these NMR findings, substitution of 7-deazaadenine at this base pair resulted in only a small (∼2-fold) decrease in the IHF-DNA binding affinity. The NMR strategy provides a new approach for resolving crystallographic ambiguity and more generally for studying the structure and dynamics of protein-DNA complexes in solution.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal 462066 , India
| | - Allison Stelling
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Yu Xu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Yi Xue
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Ying Zhang Pigli
- Biochemistry and Molecular Biology , The University of Chicago , Chicago , Illinois 60637 , United States
| | - David A Case
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Phoebe A Rice
- Biochemistry and Molecular Biology , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States.,Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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2
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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.
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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.
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3
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Nelissen FHT, Goossens EPM, Tessari M, Heus HA. Enzymatic preparation of multimilligram amounts of pure single-stranded DNA samples for material and analytical sciences. Anal Biochem 2015; 475:68-73. [PMID: 25637680 DOI: 10.1016/j.ab.2015.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/15/2022]
Abstract
We present a method for high-yield production of multimilligram amounts of pure single-stranded DNA employing rolling circle amplification (RCA) and processing by restriction enzymes. Pure and homogeneous samples are produced with minimal handling time, reagents, and waste products. The RCA method is more than twice as efficient in dNTP incorporation than conventional polymerase chain reaction in producing end product. The validity and utility of the method are demonstrated in the production of a uniformly (13)C/(15)N-labeled 38-nt cocaine aptamer DNA used in nanosensing devices.
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Affiliation(s)
- Frank H T Nelissen
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Elles P M Goossens
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Marco Tessari
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Hans A Heus
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands.
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4
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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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5
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Nelissen FHT, Girard FC, Tessari M, Heus HA, Wijmenga SS. Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion. Nucleic Acids Res 2009; 37:e114. [PMID: 19553193 PMCID: PMC2761255 DOI: 10.1093/nar/gkp540] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We demonstrate a new, efficient and easy-to-use method for enzymatic synthesis of (stereo-)specific and segmental (13)C/(15)N/(2)H isotope-labeled single-stranded DNA in amounts sufficient for NMR, based on the highly efficient self-primed PCR. To achieve this, new approaches are introduced and combined. (i) Asymmetric endonuclease double digestion of tandem-repeated PCR product. (ii) T4 DNA ligase mediated ligation of two ssDNA segments. (iii) In vitro dNTP synthesis, consisting of in vitro rNTP synthesis followed by enzymatic stereo-selective reduction of the C2' of the rNTP, and a one-pot add-up synthesis of dTTP from dUTP. The method is demonstrated on two ssDNAs: (i) a 36-nt three-way junction, selectively (13)C(9)/(15)N(3)/(2)H((1',2'',3',4',5',5''))-dC labeled and (ii) a 39-nt triple-repeat three-way junction, selectively (13)C(9)/(15)N(3)/(2)H((1',2'',3',4',5',5''))-dC and (13)C(9)/(15)N(2)/(2)H((1',2'',3',4',5',5''))-dT labeled in segment C20-C39. Their NMR spectra show the spectral simplification, while the stereo-selective (2)H-labeling in the deoxyribose of the dC-residues, straightforwardly provided assignment of their C1'-H2' and C2'-H2' resonances. The labeling protocols can be extended to larger ssDNA molecules and to more than two segments.
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Affiliation(s)
- Frank H T Nelissen
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, the Netherlands
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Martino L, Virno A, Pagano B, Virgilio A, Di Micco S, Galeone A, Giancola C, Bifulco G, Mayol L, Randazzo A. Structural and Thermodynamic Studies of the Interaction of Distamycin A with the Parallel Quadruplex Structure [d(TGGGGT)]4. J Am Chem Soc 2007; 129:16048-56. [DOI: 10.1021/ja075710k] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luigi Martino
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Ada Virno
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Bruno Pagano
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Antonella Virgilio
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Simone Di Micco
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Aldo Galeone
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Concetta Giancola
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Giuseppe Bifulco
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Luciano Mayol
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Antonio Randazzo
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
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7
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Martino L, Virno A, Randazzo A, Virgilio A, Esposito V, Giancola C, Bucci M, Cirino G, Mayol L. A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site. Nucleic Acids Res 2006; 34:6653-62. [PMID: 17145716 PMCID: PMC1751544 DOI: 10.1093/nar/gkl915] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5'-5' inversion of polarity site, namely d(3'GGT5'-5'TGGTGTGGTTGG3'), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3'GGT5'-5'TGGTGTGGTTGG3') is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4 degrees C higher than the corresponding unmodified TBA. d(3'GGT5'-5'TGGTGTGGTTGG3') continues to display an anticoagulant activity, even if decreased with respect to the TBA.
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Affiliation(s)
| | - Ada Virno
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonio Randazzo
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonella Virgilio
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | - Veronica Esposito
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | | | - Mariarosaria Bucci
- Dipartimento di Farmacologia Sperimentale, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | - Giuseppe Cirino
- Dipartimento di Farmacologia Sperimentale, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’via D. Montesano 49, I-80131 Napoli, Italy
- To whom correspondence should be addressed. Tel: +39 081 678508; Fax: +39 081 678552;
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8
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René B, Masliah G, Zargarian L, Mauffret O, Fermandjian S. General method of preparation of uniformly 13C, 15N-labeled DNA fragments for NMR analysis of DNA structures. JOURNAL OF BIOMOLECULAR NMR 2006; 36:137-46. [PMID: 17019642 DOI: 10.1007/s10858-006-9075-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 07/27/2006] [Indexed: 05/12/2023]
Abstract
(13)C, (15)N labeling of biomolecules allows easier assignments of NMR resonances and provides a larger number of NMR parameters, which greatly improves the quality of DNA structures. However, there is no general DNA-labeling procedure, like those employed for proteins and RNAs. Here, we describe a general and widely applicable approach designed for preparation of isotopically labeled DNA fragments that can be used for NMR studies. The procedure is based on the PCR amplification of oligonucleotides in the presence of labeled deoxynucleotides triphosphates. It allows great flexibility thanks to insertion of a short DNA sequence (linker) between two repeats of DNA sequence to study. Size and sequence of the linker are designed as to create restriction sites at the junctions with DNA of interest. DNA duplex with desired sequence and size is released upon enzymatic digestion of the PCR product. The suitability of the procedure is validated through the preparation of two biological relevant DNA fragments.
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Affiliation(s)
- Brigitte René
- Département de Biologie et Pharmacologie Structurales, UMR 8113 CNRS - LBPA Ecole Normale Supérieure de Cachan, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805, Villejuif Cedex, France
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9
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Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J Mol Biol 2005; 356:1137-51. [PMID: 16406070 DOI: 10.1016/j.jmb.2005.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2005] [Revised: 11/30/2005] [Accepted: 12/02/2005] [Indexed: 11/29/2022]
Abstract
The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.
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Affiliation(s)
- Jamie M Baird-Titus
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati, OH 45267-0524, USA
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10
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Kojima C, Ono A, Ono A, Kainosho M. Solid-phase synthesis of selectively labeled DNA: applications for multidimensional nuclear magnetic resonance spectroscopy. Methods Enzymol 2002; 338:261-83. [PMID: 11460552 DOI: 10.1016/s0076-6879(02)38224-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The solid-phase chemical synthesis method has a strong advantage over the enzymatic method for preparing selectively labeled DNA oligomers. Atom-specific and fully labeled 2'-deoxynucleosides are economically prepared with routinely available isotope precursors using this synthetic route. Special DNA oligomers prepared by advanced labeling techniques are needed for advanced NMR applications, and chemical synthesis is the method of choice to respond to such demands. As a summary of this chapter, two tables are given. Table I lists the labeled nucleosides reported to be available by chemical syntheses. Table II lists the NMR studies using labeled DNA oligomers that were prepared by chemical syntheses.
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Affiliation(s)
- C Kojima
- Department of Chemistry, Japan Science and Technology Corporation & Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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11
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Riek R. Characterization of hydrogen bond lengths in Watson-Crick base pairs by cross-correlated relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 149:149-153. [PMID: 11273765 DOI: 10.1006/jmre.2001.2291] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Hydrogen bond lengths in Watson-Crick base pairs can be characterized by cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond acceptor 15N. As a reference, the cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond donor 15N is used. With the two measured cross-correlated relaxation rates, an apparent hydrogen bond length can be determined, which is composed by the hydrogen bond length multiplied by a term representing the amplitude of inter-base motions. Data are presented for the 15N3-1H3...15N1 hydrogen bonds in A=T base pairs of the Antennapedia homeodomain-DNA complex with a correlation time of global rotational diffusion of 20 ns.
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Affiliation(s)
- R Riek
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, Zürich, CH-8093, Switzerland
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12
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Riek R, Pervushin K, Fernández C, Kainosho M, Wüthrich K. [(13)C,(13)C]- and [(13)C,(1)H]-TROSY in a triple resonance experiment for ribose-base and intrabase correlations in nucleic acids. J Am Chem Soc 2001; 123:658-64. [PMID: 11456577 DOI: 10.1021/ja9938276] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel TROSY (transverse relaxation-optimized spectroscopy) element is introduced that exploits cross-correlation effects between (13)C-(13)C dipole-dipole (DD) coupling and (13)C chemical shift anisotropy (CSA) of aromatic ring carbons. Although these (13)C-(13)C effects are smaller than the previously described [(13)C,(1)H]-TROSY effects for aromatic (13)C-(1)H moieties, their constructive use resulted in further transverse relaxation-optimization by up to 15% for the resonances in a 17 kDa protein-DNA complex. As a practical application, two- and three-dimensional versions of the HCN triple resonance experiment for obtaining ribose-base and intrabase correlations in the nucleotides of DNA and RNA (Sklenar, V.; Peterson, R. D.; Rejante, M. R.; Feigon, J. J. Biomol. NMR 1993, 3, 721-727) have been implemented with [(13)C,(1)H]- and [(13)C,(13)C]-TROSY elements to reduce the rate of transverse relaxation during the polarization transfers between ribose (13)C1' and base (15)N1/9 spins, and between (13)C6/8 and N1/9 within the bases. The resulting TROSY-HCN experiment is user-friendly, with a straightforward, robust experimental setup. Compared to the best previous implementations of the HCN experiment, 2-fold and 5-fold sensitivity enhancements have been achieved for ribose-base and intrabase connectivities, respectively, for (13)C,(15)N-labeled nucleotides in structures with molecular weights of 10 and 17 kDa. TROSY-HCN experiments should be applicable also with significantly larger molecular weights. By using modified TROSY-HCN schemes, the origins of the sensitivity gains have been analyzed.
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Affiliation(s)
- R Riek
- Institute für Molekularbiologie and Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093 Zürich, Switzerland
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13
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Riek R, Pervushin K, Wüthrich K. TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution. Trends Biochem Sci 2000; 25:462-8. [PMID: 11050425 DOI: 10.1016/s0968-0004(00)01665-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
TROSY and CRINEPT are new techniques for solution NMR studies of molecular and supramolecular structures. They allow the collection of high-resolution spectra of structures with molecular weights >100 kDa, significantly extending the range of macromolecular systems that can be studied by NMR in solution. TROSY has already been used to map protein-protein interfaces, to conduct structural studies on membrane proteins and to study nucleic acid conformations in multimolecular assemblies. These techniques will help us to investigate the conformational states of individual macromolecular components and will support de novo protein structure determination in large supramolecular structures.
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Affiliation(s)
- R Riek
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland
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Szyperski T, Fernández C, Ono A, Wüthrich K, Kainosho M. The 2D [31P] spin-echo-difference constant-time [13C, 1H]-HMQC experiment for simultaneous determination of 3J(H3'P) and 3J(C4'P) in 13C-labeled nucleic acids and their protein complexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 140:491-494. [PMID: 10497056 DOI: 10.1006/jmre.1999.1870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A two-dimensional [31P] spin-echo-difference constant-time [13C, 1H]-HMQC experiment (2D [31P]-sedct-[13C, 1H]-HMQC) is introduced for measurements of 3J(C4'P) and 3J(H3'P) scalar couplings in large 13C-labeled nucleic acids and in DNA-protein complexes. This experiment makes use of the fact that 1H-13C multiple-quantum coherences in macromolecules relax more slowly than the corresponding 13C single-quantum coherences. 3J(C4'P) and 3J(H3'P) are related via Karplus-type functions with the phosphodiester torsion angles beta and epsilon, respectively, and their experimental assessment therefore contributes to further improved quality of NMR solution structures. Data are presented for a uniformly 13C, 15N-labeled 14-base-pair DNA duplex, both free in solution and in a 17-kDa protein-DNA complex.
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Affiliation(s)
- T Szyperski
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, CH-8093, Switzerland
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15
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Fernández C, Szyperski T, Billeter M, Ono A, Iwai H, Kainosho M, Wüthrich K. Conformational changes of the BS2 operator DNA upon complex formation with the Antennapedia homeodomain studied by NMR with 13C/15N-labeled DNA. J Mol Biol 1999; 292:609-17. [PMID: 10497025 DOI: 10.1006/jmbi.1999.2987] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The NMR structures have been determined for a 13C/15N doubly labeled 14 base-pair DNA duplex comprising the BS2 operator sequence both free in solution and in the complex with the Antennapedia homeodomain. The impact of the DNA labeling is assessed from comparison with a previous structure of the same complex that was determined using isotope labeling only for the protein. Differences between the two structure determinations are nearly completely limited to the DNA, which retains the global B -conformation of the free DNA also in the complex. Local protein-induced conformational changes are a narrowing of the minor groove due to the interaction with the N-terminal arm of the homeodomain, and changes of the sugar puckers of the deoxyriboses G5 and C6, which are apparently induced by van der Waals interactions with Tyr25, and with Gln50 and Arg53, respectively. The high conservation of these amino acid residues in homeodomains suggests that protein-induced shifts in some sugar puckers contribute to the affinity of homeodomains to their cognate DNA. The data obtained here with the Antennapedia homeodomain-DNA complex clearly show that nucleic acid isotope-labeling can support detailed conformational characterization of DNA in complexes with proteins, which will be indispensable for structure determinations of complexes containing globally distorted DNA conformations.
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Affiliation(s)
- C Fernández
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, Zürich, CH-8093, Switzerland
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16
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Ippel H, Larsson G, Behravan G, Zdunek J, Lundqvist M, Schleucher J, Lycksell PO, Wijmenga S. The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains. J Mol Biol 1999; 288:689-703. [PMID: 10329173 DOI: 10.1006/jmbi.1999.2718] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for DNA recognition. We have determined a high-quality nuclear magnetic resonance (NMR) structure of the DNA-binding homeodomain of the insulin gene enhancer protein Isl-1 (Isl-1-HD). It forms the first solution structure of a homeodomain from the LIM family. It contains a well-defined inner core (residues 12-55) consisting of the classical three-helix structure observed in other homeodomains. The N terminus is unstructured up to residue 8, while the C terminus gradually becomes unstructured from residue 55 onwards. Some flexibility is evident in the loop parts of the inner core. Isl-1-HD has, despite its low sequence identity (23-34 %), a structure that is strikingly similar to that of the other homeodomains with known three-dimensional structures. Detailed analysis of Isl-1-HD and the other homeodomains rationalizes the differences in their temperature stability and explains the low stability of the Isl-1-HD in the free state (tm 22-30 degrees C). Upon DNA binding, a significant stabilization occurs (tm>55 degrees C). The low stability of Isl-1-HD (and other mammalian homeodomains) suggests that in vivo Isl-1-HD recognizes its cognate DNA from its unfolded state.
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Affiliation(s)
- H Ippel
- Department of Medical Biochemistry and Biophysics, Umeâ University, Umeâ, S 901 87, Sweden
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17
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Milecki J, Zamaratski E, Maltseva TV, Földesi A, Adamiak RW, Chattopadhyaya J. The first example of sequence-specific non-uniformly 13C5 labelled RNA: Synthesis of the 29mer HIV-1 TAR RNA with 13C Relaxation Window. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00294-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Masse JE, Allain FHT, Yen YM, Johnson RC, Feigon J. Use of 13C,15N-Labeled DNA in a Non-Sequence-Specific Protein−DNA Complex Resolves Ambiguous Assignments of Intermolecular NOEs. J Am Chem Soc 1999. [DOI: 10.1021/ja9839926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James E. Masse
- Department of Chemistry and Biochemistry Molecular Biology Institute and Department of Biological Chemistry University of California, Los Angeles, California 90095-1569
| | - Frédéric H-T. Allain
- Department of Chemistry and Biochemistry Molecular Biology Institute and Department of Biological Chemistry University of California, Los Angeles, California 90095-1569
| | - Yi-Meng Yen
- Department of Chemistry and Biochemistry Molecular Biology Institute and Department of Biological Chemistry University of California, Los Angeles, California 90095-1569
| | - Reid C. Johnson
- Department of Chemistry and Biochemistry Molecular Biology Institute and Department of Biological Chemistry University of California, Los Angeles, California 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry Molecular Biology Institute and Department of Biological Chemistry University of California, Los Angeles, California 90095-1569
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19
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Pervushin K, Ono A, Fernández C, Szyperski T, Kainosho M, Wüthrich K. NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci U S A 1998; 95:14147-51. [PMID: 9826668 PMCID: PMC24341 DOI: 10.1073/pnas.95.24.14147] [Citation(s) in RCA: 265] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes the NMR observation of 15N---15N and 1H---15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs in a DNA duplex, hJNN and hJHN. These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [15N,1H]-transverse relaxation-optimized spectroscopy (TROSY) with a 15N-labeled 14-mer DNA duplex was used to measure hJNN, which is in the range 6-7 Hz, and the two-dimensional hJNN-correlation-[15N,1H]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related 15N spins and to observe, for the first time, hJHN scalar couplings, with values in the range 2-3.6 Hz. TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids.
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Affiliation(s)
- K Pervushin
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule, Hönggerberg CH-8093 Zürich, Switzerland
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