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Agnarelli A, El Omari K, Duman R, Wagner A, Mancini EJ. Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2021; 77:202-207. [PMID: 34196610 PMCID: PMC8248823 DOI: 10.1107/s2053230x21006506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
Abstract
Solution of the structure of the DNA-binding domain of interferon regulatory factor 4 bound to its interferon-stimulated response element by native intrinsic phosphorus and sulfur single-wavelength anomalous dispersion methods (native SAD) is described. Pivotal to the regulation of key cellular processes such as the transcription, replication and repair of DNA, DNA-binding proteins play vital roles in all aspects of genetic activity. The determination of high-quality structures of DNA-binding proteins, particularly those in complexes with DNA, provides crucial insights into the understanding of these processes. The presence in such complexes of phosphate-rich oligonucleotides offers the choice of a rapid method for the routine solution of DNA-binding proteins through the use of long-wavelength beamlines such as I23 at Diamond Light Source. This article reports the use of native intrinsic phosphorus and sulfur single-wavelength anomalous dispersion methods to solve the complex of the DNA-binding domain (DBD) of interferon regulatory factor 4 (IRF4) bound to its interferon-stimulated response element (ISRE). The structure unexpectedly shows three molecules of the IRF4 DBD bound to one ISRE. The sole reliance on native intrinsic anomalous scattering elements that belong to DNA–protein complexes renders the method of general applicability to a large number of such protein complexes that cannot be solved by molecular replacement or by other phasing methods.
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Affiliation(s)
- Alessandro Agnarelli
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
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Zhang Y, El Omari K, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 2020; 48:9886-9898. [PMID: 32453431 PMCID: PMC7515729 DOI: 10.1093/nar/gkaa439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.
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Affiliation(s)
- Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
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Conlon PF, Eguaogie O, Wilson JJ, Sweet JST, Steinhoegl J, Englert K, Hancox OGA, Law CJ, Allman SA, Tucker JHR, Hall JP, Vyle JS. Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography. Chem Sci 2019; 10:10948-10957. [PMID: 32190252 PMCID: PMC7066676 DOI: 10.1039/c9sc04098f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/11/2019] [Indexed: 01/20/2023] Open
Abstract
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
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Affiliation(s)
- Patrick F Conlon
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Olga Eguaogie
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jordan J Wilson
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jamie S T Sweet
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Julian Steinhoegl
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Klaudia Englert
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - Oliver G A Hancox
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Christopher J Law
- School of Biological Sciences , Queen's University Belfast , 15 Chlorine Gardens , Belfast BT9 5AH , UK
| | - Sarah A Allman
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - James H R Tucker
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - James P Hall
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
- Diamond Light Source , Chilton , Didcot , Oxfordshire OX11 0DE , UK
| | - Joseph S Vyle
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
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