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Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. CRISPR-Cas9 bends and twists DNA to read its sequence. Nat Struct Mol Biol 2022; 29:395-402. [PMID: 35422516 PMCID: PMC9189902 DOI: 10.1038/s41594-022-00756-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022]
Abstract
In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9-RNA-DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 'reads' snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.
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Affiliation(s)
- Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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2
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Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS. Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol 2022; 208:381-389. [PMID: 35337914 DOI: 10.1016/j.ijbiomac.2022.03.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany
| | - Jun-Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Kumoh National Institute of Technology, 61, Daehak-ro, Gumi, Gyeongbuk 39177, Republic of Korea
| | - Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thi Yen Ly Huynh
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, Hwasun, Jeonnam 58128, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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3
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Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. J Chem Inf Model 2017; 57:2020-2026. [PMID: 28696686 DOI: 10.1021/acs.jcim.7b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Free energy simulations are presented to probe the energetic coupling between DNA bending and the flipping of a central thymine in double stranded DNA 13mers. The energetics are shown to depend on the neighboring base pairs, and upstream C or T or downstream C tended to make flipping more costly. Flipping to the major groove side was generally preferred. Bending aids flipping, by pushing the system up in free energy, but for small and intermediate bending angles the two were uncorrelated. At higher bending angles, bending and flipping became correlated, and bending primed the system for base flipping toward the major groove. Flipping of the 6-4 pyrimidine-pyrimidone and pyrimidine dimer photoproducts is shown to be more facile than for undamaged DNA. For the damages, major groove flipping was preferred, and DNA bending was much facilitated in the 6-4 pyrimidine-pyrimidone damaged system. Aspects of the calculations were verified by structural analyses of protein-DNA complexes with flipped bases.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
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Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process. Mol Cell 2016; 64:376-387. [PMID: 27720644 DOI: 10.1016/j.molcel.2016.09.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 07/18/2016] [Accepted: 09/01/2016] [Indexed: 12/25/2022]
Abstract
Nucleotide excision repair (NER) is an evolutionarily conserved mechanism that processes helix-destabilizing and/or -distorting DNA lesions, such as UV-induced photoproducts. Here, we investigate the dynamic protein-DNA interactions during the damage recognition step using single-molecule fluorescence microscopy. Quantum dot-labeled Rad4-Rad23 (yeast XPC-RAD23B ortholog) forms non-motile complexes or conducts a one-dimensional search via either random diffusion or constrained motion. Atomic force microcopy analysis of Rad4 with the β-hairpin domain 3 (BHD3) deleted reveals that this motif is non-essential for damage-specific binding and DNA bending. Furthermore, we find that deletion of seven residues in the tip of β-hairpin in BHD3 increases Rad4-Rad23 constrained motion at the expense of stable binding at sites of DNA lesions, without diminishing cellular UV resistance or photoproduct repair in vivo. These results suggest a distinct intermediate in the damage recognition process during NER, allowing dynamic DNA damage detection at a distance.
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5
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Kanwar N, Roberts GA, Cooper LP, Stephanou AS, Dryden DTF. The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA. Nucleic Acids Res 2016; 44:4289-303. [PMID: 27095198 PMCID: PMC4872106 DOI: 10.1093/nar/gkw234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/24/2016] [Indexed: 11/13/2022] Open
Abstract
The protein Ocr (overcome classical restriction) from bacteriophage T7 acts as a mimic of DNA and inhibits all Type I restriction/modification (RM) enzymes. Ocr is a homodimer of 116 amino acids and adopts an elongated structure that resembles the shape of a bent 24 bp DNA molecule. Each monomer includes 34 acidic residues and only six basic residues. We have delineated the mimicry of Ocr by focusing on the electrostatic contribution of its negatively charged amino acids using directed evolution of a synthetic form of Ocr, termed pocr, in which all of the 34 acidic residues were substituted for a neutral amino acid. In vivo analyses confirmed that pocr did not display any antirestriction activity. Here, we have subjected the gene encoding pocr to several rounds of directed evolution in which codons for the corresponding acidic residues found in Ocr were specifically re-introduced. An in vivo selection assay was used to detect antirestriction activity after each round of mutation. Our results demonstrate the variation in importance of the acidic residues in regions of Ocr corresponding to different parts of the DNA target which it is mimicking and for the avoidance of deleterious effects on the growth of the host.
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Affiliation(s)
- Nisha Kanwar
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Augoustinos S Stephanou
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - David T F Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
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6
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Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction–modification enzyme. Biochem Biophys Res Commun 2014; 449:120-5. [DOI: 10.1016/j.bbrc.2014.04.162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/23/2022]
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7
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Zavilgelsky GB, Kotova VY. Antirestriction activity of the monomeric and dimeric forms of T7 Ocr. Mol Biol 2014. [DOI: 10.1134/s0026893313060174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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9
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Chen K, Reuter M, Sanghvi B, Roberts GA, Cooper LP, Tilling M, Blakely GW, Dryden DTF. ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:505-11. [PMID: 24368349 PMCID: PMC3969726 DOI: 10.1016/j.bbapap.2013.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/11/2013] [Accepted: 12/13/2013] [Indexed: 12/11/2022]
Abstract
Anti-restriction and anti-modification (anti-RM) is the ability to prevent cleavage by DNA restriction–modification (RM) systems of foreign DNA entering a new bacterial host. The evolutionary consequence of anti-RM is the enhanced dissemination of mobile genetic elements. Homologues of ArdA anti-RM proteins are encoded by genes present in many mobile genetic elements such as conjugative plasmids and transposons within bacterial genomes. The ArdA proteins cause anti-RM by mimicking the DNA structure bound by Type I RM enzymes. We have investigated ArdA proteins from the genomes of Enterococcus faecalis V583, Staphylococcus aureus Mu50 and Bacteroides fragilis NCTC 9343, and compared them to the ArdA protein expressed by the conjugative transposon Tn916. We find that despite having very different structural stability and secondary structure content, they can all bind to the EcoKI methyltransferase, a core component of the EcoKI Type I RM system. This finding indicates that the less structured ArdA proteins become fully folded upon binding. The ability of ArdA from diverse mobile elements to inhibit Type I RM systems from other bacteria suggests that they are an advantage for transfer not only between closely-related bacteria but also between more distantly related bacterial species. Diverse ArdA proteins all target the EcoKI Type I DNA modification enzyme. ArdA proteins have variable secondary structure content. ArdA all bind equally well to EcoKI despite stability variations.
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Affiliation(s)
- Kai Chen
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Marcel Reuter
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Bansi Sanghvi
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Matthew Tilling
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
| | - Garry W Blakely
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JR, UK
| | - David T F Dryden
- EaStCHEM School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
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10
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Ma L, Chen K, Clarke DJ, Nortcliffe CP, Wilson GG, Edwardson JM, Morton AJ, Jones AC, Dryden DTF. Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats. Nucleic Acids Res 2013; 41:4999-5009. [PMID: 23525471 PMCID: PMC3643589 DOI: 10.1093/nar/gkt176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The type II restriction endonuclease TseI recognizes the DNA target sequence 5′-G^CWGC-3′ (where W = A or T) and cleaves after the first G to produce fragments with three-base 5′-overhangs. We have determined that it is a dimeric protein capable of cleaving not only its target sequence but also one containing A:A or T:T mismatches at the central base pair in the target sequence. The cleavage of targets containing these mismatches is as efficient as cleavage of the correct target sequence containing a central A:T base pair. The cleavage mechanism does not apparently use a base flipping mechanism as found for some other type II restriction endonuclease recognizing similarly degenerate target sequences. The ability of TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated with Huntington’s disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).
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Affiliation(s)
- Long Ma
- EaStChem School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
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11
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Roberts GA, Stephanou AS, Kanwar N, Dawson A, Cooper LP, Chen K, Nutley M, Cooper A, Blakely GW, Dryden DTF. Exploring the DNA mimicry of the Ocr protein of phage T7. Nucleic Acids Res 2012; 40:8129-43. [PMID: 22684506 PMCID: PMC3439906 DOI: 10.1093/nar/gks516] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 11/30/2022] Open
Abstract
DNA mimic proteins have evolved to control DNA-binding proteins by competing with the target DNA for binding to the protein. The Ocr protein of bacteriophage T7 is the most studied DNA mimic and functions to block the DNA-binding groove of Type I DNA restriction/modification enzymes. This binding prevents the enzyme from cleaving invading phage DNA. Each 116 amino acid monomer of the Ocr dimer has an unusual amino acid composition with 34 negatively charged side chains but only 6 positively charged side chains. Extensive mutagenesis of the charges of Ocr revealed a regression of Ocr activity from wild-type activity to partial activity then to variants inactive in antirestriction but deleterious for cell viability and lastly to totally inactive variants with no deleterious effect on cell viability. Throughout the mutagenesis the Ocr mutant proteins retained their folding. Our results show that the extreme bias in charged amino acids is not necessary for antirestriction activity but that less charged variants can affect cell viability by leading to restriction proficient but modification deficient cell phenotypes.
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Affiliation(s)
- Gareth A. Roberts
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Augoustinos S. Stephanou
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Nisha Kanwar
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Angela Dawson
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Laurie P. Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Kai Chen
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Margaret Nutley
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Alan Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Garry W. Blakely
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - David T. F. Dryden
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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13
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Roberts GA, Cooper LP, White JH, Su TJ, Zipprich JT, Geary P, Kennedy C, Dryden DTF. An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme. Nucleic Acids Res 2011; 39:7667-76. [PMID: 21685455 PMCID: PMC3177214 DOI: 10.1093/nar/gkr480] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Type I DNA restriction/modification systems are oligomeric enzymes capable of switching between a methyltransferase function on hemimethylated host DNA and an endonuclease function on unmethylated foreign DNA. They have long been believed to not turnover as endonucleases with the enzyme becoming inactive after cleavage. Cleavage is preceded and followed by extensive ATP hydrolysis and DNA translocation. A role for dissociation of subunits to allow their reuse has been proposed for the EcoR124I enzyme. The EcoKI enzyme is a stable assembly in the absence of DNA, so recycling was thought impossible. Here, we demonstrate that EcoKI becomes unstable on long unmethylated DNA; reuse of the methyltransferase subunits is possible so that restriction proceeds until the restriction subunits have been depleted. We observed that RecBCD exonuclease halts restriction and does not assist recycling. We examined the DNA structure required to initiate ATP hydrolysis by EcoKI and find that a 21-bp duplex with single-stranded extensions of 12 bases on either side of the target sequence is sufficient to support hydrolysis. Lastly, we discuss whether turnover is an evolutionary requirement for restriction, show that the ATP hydrolysis is not deleterious to the host cell and discuss how foreign DNA occasionally becomes fully methylated by these systems.
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14
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Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2'-deoxyguanosine as a fluorescent 2'-deoxyguanosine mimic for investigating DNA hybridization and topology. Angew Chem Int Ed Engl 2011; 50:5392-6. [PMID: 21542071 DOI: 10.1002/anie.201100078] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/10/2022]
Affiliation(s)
- André Nadler
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
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15
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Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2′-desoxyguanosin als fluoreszierendes 2′-Desoxyguanosin- Analogon zur Untersuchung von DNA-Hybridisierung und Topologie. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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16
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Chen K, Roberts GA, Stephanou AS, Cooper LP, White JH, Dryden DTF. Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes. Biochem Biophys Res Commun 2010; 398:254-9. [PMID: 20599730 PMCID: PMC2914225 DOI: 10.1016/j.bbrc.2010.06.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 06/16/2010] [Indexed: 01/29/2023]
Abstract
We describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA sequence-specificity subunit of the Type I DNA modification methyltransferase M.EcoKI. The fusion expresses well in vivo and assembles with the two HsdM modification subunits. The fusion protein functions as a sequence-specific DNA methyltransferase protecting DNA against digestion by the EcoKI restriction endonuclease. The purified enzyme shows Förster resonance energy transfer to fluorescently-labelled DNA duplexes containing the target sequence and to fluorescently-labelled ocr protein, a DNA mimic that binds to the M.EcoKI enzyme. Distances determined from the energy transfer experiments corroborate the structural model of M.EcoKI.
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Affiliation(s)
- Kai Chen
- School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JJ, UK
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17
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Madhusoodanan UK, Rao DN. Diversity of DNA methyltransferases that recognize asymmetric target sequences. Crit Rev Biochem Mol Biol 2010; 45:125-45. [PMID: 20184512 DOI: 10.3109/10409231003628007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.
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18
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Stephanou AS, Roberts GA, Cooper LP, Clarke DJ, Thomson AR, MacKay CL, Nutley M, Cooper A, Dryden DT. Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification. J Mol Biol 2009; 391:565-76. [PMID: 19523474 PMCID: PMC2806950 DOI: 10.1016/j.jmb.2009.06.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 12/02/2022]
Abstract
The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an approximately 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove approximately 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to approximately 800-fold.
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Key Words
- ocr, overcome classical restriction
- r/m, restriction/modification
- edc, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride
- hobt, hydroxybenzotriazole
- ms, mass spectrometry
- maldi-tof, matrix-assisted laser desorption/ionization time of flight
- ft-icr, fourier transform ion cyclotron resonance
- gdmcl, guanidinium hydrochloride
- sam, s-adenosyl-l-methionine
- itc, isothermal titration calorimetry
- wt, wild type
- dna mimic
- chemical modification
- restriction/modification system
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Affiliation(s)
| | - Gareth A. Roberts
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - Laurie P. Cooper
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - David J. Clarke
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - Andrew R. Thomson
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - C. Logan MacKay
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - Margaret Nutley
- West Chem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alan Cooper
- West Chem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - David T.F. Dryden
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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19
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Neaves KJ, Cooper LP, White JH, Carnally SM, Dryden DTF, Edwardson JM, Henderson RM. Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping. Nucleic Acids Res 2009; 37:2053-63. [PMID: 19223329 PMCID: PMC2665228 DOI: 10.1093/nar/gkp042] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Atomic force microscopy (AFM) allows the study of single protein–DNA interactions such as those observed with the Type I Restriction–Modification systems. The mechanisms employed by these systems are complicated and understanding them has proved problematic. It has been known for years that these enzymes translocate DNA during the restriction reaction, but more recent AFM work suggested that the archetypal EcoKI protein went through an additional dimerization stage before the onset of translocation. The results presented here extend earlier findings confirming the dimerization. Dimerization is particularly common if the DNA molecule contains two EcoKI recognition sites. DNA loops with dimers at their apex form if the DNA is sufficiently long, and also form in the presence of ATPγS, a non-hydrolysable analogue of the ATP required for translocation, indicating that the looping is on the reaction pathway of the enzyme. Visualization of specific DNA loops in the protein–DNA constructs was achieved by improved sample preparation and analysis techniques. The reported dimerization and looping mechanism is unlikely to be exclusive to EcoKI, and offers greater insight into the detailed functioning of this and other higher order assemblies of proteins operating by bringing distant sites on DNA into close proximity via DNA looping.
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Affiliation(s)
- Kelly J Neaves
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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20
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Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 2009; 37:762-70. [PMID: 19074193 PMCID: PMC2647291 DOI: 10.1093/nar/gkn988] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 11/20/2008] [Accepted: 11/21/2008] [Indexed: 12/25/2022] Open
Abstract
Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.
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Affiliation(s)
- Christopher K. Kennaway
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Agnieszka Obarska-Kosinska
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - John H. White
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Irina Tuszynska
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Laurie P. Cooper
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Janusz M. Bujnicki
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - John Trinick
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - David T. F. Dryden
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
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21
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A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7. Biochem Biophys Res Commun 2008; 378:129-32. [PMID: 19013430 DOI: 10.1016/j.bbrc.2008.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 11/24/2022]
Abstract
The ocr protein of bacteriophage T7 is a structural and electrostatic mimic of approximately 24 base pairs of double-stranded B-form DNA. As such, it inhibits all Type I restriction and modification (R/M) enzymes by blocking their DNA binding grooves and inactivates them. This allows the infection of the bacterial cell by T7 to proceed unhindered by the action of the R/M defence system. We have mutated aspartate and glutamate residues on the surface of ocr to investigate their contribution to the tight binding between the EcoKI Type I R/M enzyme and ocr. Contrary to expectations, all of the single and double site mutations of ocr constructed were active as anti-R/M proteins in vivo and in vitro indicating that the mimicry of DNA by ocr is very resistant to change.
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22
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Youngblood B, Bonnist E, Dryden DTF, Jones AC, Reich NO. Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies. Nucleic Acids Res 2008; 36:2917-25. [PMID: 18385156 PMCID: PMC2396439 DOI: 10.1093/nar/gkn131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
M.EcoRI, a bacterial sequence-specific S-adenosyl-l-methionine-dependent DNA methyltransferase, relies on a complex conformational mechanism to achieve its remarkable specificity, including DNA bending, base flipping and intercalation into the DNA. Using transient fluorescence and fluorescence lifetime studies with cognate and noncognate DNA, we have characterized several reaction intermediates involving the WT enzyme. Similar studies with a bending-impaired, enhanced-specificity M.EcoRI mutant show minimal differences with the cognate DNA, but significant differences with noncognate DNA. These results provide a plausible explanation of the way in which destabilization of reaction intermediates can lead to changes in substrate specificity.
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Affiliation(s)
- Ben Youngblood
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106-9510, USA
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23
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Bahr M, Valis L, Wagenknecht HA, Weinhold E. DNA labelling topologies for monitoring DNA-protein complex formation by fluorescence anisotropy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1581-4. [PMID: 18066831 DOI: 10.1080/15257770701547347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this work, fluorescence anisotropy was used to study DNA binding of the DNA methyltransferase M.TaqI. For this purpose short DNA molecules labelled with three different fluorophores (Cy3, thiazole orange, and ethidium bromide) were prepared in various topologies and their suitability for detection of DNA-protein complex formation was investigated.
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Affiliation(s)
- Matthias Bahr
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
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24
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Yuan C, Lou XW, Rhoades E, Chen H, Archer LA. T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res 2007; 35:5294-302. [PMID: 17686784 PMCID: PMC2018621 DOI: 10.1093/nar/gkm582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.
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Affiliation(s)
- Chongli Yuan
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Xiong Wen Lou
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Rhoades
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Huimin Chen
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lynden A. Archer
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- *To whom correspondence should be addressed. +1 607 254 8825+1 607 255 9166
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25
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Bouvier B, Grubmüller H. A molecular dynamics study of slow base flipping in DNA using conformational flooding. Biophys J 2007; 93:770-86. [PMID: 17496048 PMCID: PMC1913169 DOI: 10.1529/biophysj.106.091751] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication. Much remains unknown about this elementary step, despite a wealth of experimental and theoretical studies. From the theoretical point of view, the involved timescale of milliseconds or longer requires the use of enhanced sampling techniques. In contrast to previous theoretical studies employing umbrella sampling along a predefined flipping coordinate, this study attempts to induce flipping without prior knowledge of the pathway, using information from a molecular dynamics simulation of a B-DNA fragment and the conformational flooding method. The relevance to base flipping of the principal components of the simulation is assayed, and a combination of modes optimally related to the flipping of the base through either helical groove is derived for each of the two bases of the central guanine-cytosine basepair. By applying an artificial flooding potential along these collective coordinates, the flipping mechanism is accelerated to within the scope of molecular dynamics simulations. The associated free energy surface is found to feature local minima corresponding to partially flipped states, particularly relevant to flipping in isolated DNA; further transitions from these minima to the fully flipped conformation are accelerated by additional flooding potentials. The associated free energy profiles feature similar barrier heights for both bases and pathways; the flipped state beyond is a broad and rugged attraction basin, only a few kcal/mol higher in energy than the closed conformation. This result diverges from previous works but echoes some aspects of recent experimental findings, justifying the need for novel approaches to this difficult problem: this contribution represents a first step in this direction. Important structural factors involved in flipping, both local (sugar-phosphate backbone dihedral angles) and global (helical axis bend), are also identified.
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Affiliation(s)
- Benjamin Bouvier
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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26
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Bellamy SR, Krusong K, Baldwin GS. A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping. Nucleic Acids Res 2007; 35:1478-87. [PMID: 17284454 PMCID: PMC1865060 DOI: 10.1093/nar/gkm018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Uracil DNA glycosylase (UNG) is the primary enzyme for the removal of uracil from the genome of many organisms. A key question is how the enzyme is able to scan large quantities of DNA in search of aberrant uracil residues. Central to this is the mechanism by which it flips the target nucleotide out of the DNA helix and into the enzyme-active site. Both active and passive mechanisms have been proposed. Here, we report a rapid kinetic analysis using two fluorescent chromophores to temporally resolve DNA binding and base-flipping with DNA substrates of different sequences. This study demonstrates the importance of the protein–DNA interface in the search process and indicates an active mechanism by which UNG glycosylase searches for uracil residues.
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Affiliation(s)
| | | | - Geoff S. Baldwin
- *To whom correspondence should be addressed. +(44) 20 7594 5228+(44) 20 7584 2056
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27
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Youngblood B, Reich NO. Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI. J Biol Chem 2006; 281:26821-31. [PMID: 16845123 DOI: 10.1074/jbc.m603388200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Changes in DNA bending and base flipping in a previously characterized specificity-enhanced M.EcoRI DNA adenine methyltransferase mutant suggest a close relationship between precatalytic conformational transitions and specificity (Allan, B. W., Garcia, R., Maegley, K., Mort, J., Wong, D., Lindstrom, W., Beechem, J. M., and Reich, N. O. (1999) J. Biol. Chem. 274, 19269-19275). The direct measurement of the kinetic rate constants for DNA bending, intercalation, and base flipping with cognate and noncognate substrates (GAATTT, GGATTC) of wild type M.EcoRI using fluorescence resonance energy transfer and 2-aminopurine fluorescence studies reveals that DNA bending precedes both intercalation and base flipping, and base flipping precedes intercalation. Destabilization of these intermediates provides a molecular basis for understanding how conformational transitions contribute to specificity. The 3500- and 23,000-fold decreases in sequence specificity for noncognate sites GAATTT and GGATTC are accounted for largely by an approximately 2500-fold increase in the reverse rate constants for intercalation and base flipping, respectively. Thus, a predominant contribution to specificity is a partitioning of enzyme intermediates away from the Michaelis complex prior to catalysis. Our results provide a basis for understanding enzyme specificity and, in particular, sequence-specific DNA modification. Because many DNA methyltransferases and DNA repair enzymes induce similar DNA distortions, these results are likely to be broadly relevant.
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Affiliation(s)
- Ben Youngblood
- Program in Biomolecular Science and Engineering, Department of Chemistry and Biochemistry, University of California, Santa Barbara 93106-9510, USA
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28
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Shieh FK, Youngblood B, Reich NO. The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI. J Mol Biol 2006; 362:516-27. [PMID: 16926025 DOI: 10.1016/j.jmb.2006.07.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Revised: 07/13/2006] [Accepted: 07/14/2006] [Indexed: 10/24/2022]
Abstract
Arg165 forms part of a previously identified base flipping motif in the bacterial DNA cytosine methyltransferase, M.HhaI. Replacement of Arg165 with Ala has no detectable effect on either DNA or AdoMet affinity, yet causes the base flipping and restacking transitions to be decreased approximately 16 and 190-fold respectively, thus confirming the importance of this motif. However, these kinetic changes cannot account for the mutant's observed 10(5)-fold decreased catalytic rate. The mutant enzyme/cognate DNA cocrystal structure (2.79 A resolution) shows the target cytosine to be positioned approximately 30 degrees into the major groove, which is consistent with a major groove pathway for nucleotide flipping. The pyrimidine-sugar chi angle is rotated to approximately +171 degrees, from a range of -95 degrees to -120 degrees in B DNA, and -77 degrees in the WT M.HhaI complex. Thus, Arg165 is important for maintaining the cytosine positioned for nucleophilic attack by Cys81. The cytosine sugar pucker is in the C2'-endo-C3'-exo (South conformation), in contrast to the previously reported C3'-endo (North conformation) described for the original 2.70 A resolution cocrystal structure of the WT M.HhaI/DNA complex. We determined a high resolution structure of the WT M.HhaI/DNA complex (1.96 A) to better determine the sugar pucker. This new structure is similar to the original, lower resolution WT M.HhaI complex, but shows that the sugar pucker is O4'-endo (East conformation), intermediate between the South and North conformers. In summary, Arg165 plays significant roles in base flipping, cytosine positioning, and catalysis. Furthermore, the previously proposed M.HhaI-mediated changes in sugar pucker may not be an important contributor to the base flipping mechanism. These results provide insights into the base flipping and catalytic mechanisms for bacterial and eukaryotic DNA methyltransferases.
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Affiliation(s)
- Fa-Kuen Shieh
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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29
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Dryden DTF. DNA mimicry by proteins and the control of enzymatic activity on DNA. Trends Biotechnol 2006; 24:378-82. [PMID: 16815576 DOI: 10.1016/j.tibtech.2006.06.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 05/03/2006] [Accepted: 06/14/2006] [Indexed: 11/18/2022]
Abstract
Cells are unable to perform any function on their DNA in the absence of proteins, and it is of vital importance that these proteins only perform their function at appropriate times during the cell cycle. Thus, DNA-binding proteins are always controlled by a wide range of other factors, primarily other proteins. These controlling factors usually block access of the protein to the DNA, often operating by simple competitive inhibition. However, it has recently been demonstrated that DNA-binding proteins can be controlled by the direct binding of the control protein to the DNA-binding site on the first protein. The structures of these control proteins have revealed that they mimic the structure and electrostatics of DNA. This review highlights the roles of DNA mimics in the control of DNA-binding proteins, suggests other possible candidate proteins using DNA mimicry, and puts forward a range of potential uses of DNA mimics.
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Affiliation(s)
- David T F Dryden
- School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK.
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30
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Obarska A, Blundell A, Feder M, Vejsadová Š, Šišáková E, Weiserová M, Bujnicki JM, Firman K. Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res 2006; 34:1992-2005. [PMID: 16614449 PMCID: PMC1435980 DOI: 10.1093/nar/gkl132] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restriction–modification (R-M) enzymes MjaXIP and MgeORF438 have provided a convenient structural template for analysis of the more extensively characterized members of this interesting family of multisubunit molecular motors. Here, we present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative modelling, followed by optimization of inter-subunit contacts by energy minimization. The model of M.EcoR124I has allowed identification of a number of functionally important residues that appear to be involved in DNA-binding. In addition, we have mapped onto the model the location of several new mutations of the hsdS gene of M.EcoR124I that were produced by misincorporation mutagenesis within the central conserved region of hsdS, we have mapped all previously identified DNA-binding mutants of TRD2 and produced a detailed analysis of the location of surface-modifiable lysines. The model structure, together with location of the mutant residues, provides a better background on which to study protein–protein and protein–DNA interactions in Type I R-M systems.
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Affiliation(s)
| | - Alex Blundell
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
| | | | - Štěpánka Vejsadová
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | - Eva Šišáková
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | - Marie Weiserová
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | | | - Keith Firman
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
- To whom all correspondence should be addressed. Tel: +44 2392 842059; Fax: +44 2392 842070;
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31
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Abstract
It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.
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