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Escouboué M, Camborde L, Jauneau A, Gaulin E, Deslandes L. Preparation of Plant Material for Analysis of Protein-Nucleic Acid Interactions by FRET-FLIM. Methods Mol Biol 2019; 1991:69-77. [PMID: 31041764 DOI: 10.1007/978-1-4939-9458-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA-binding proteins are involved in the dynamic regulation of various cellular processes such as recombination, replication, and transcription. For investigating dynamic assembly and disassembly of molecular complexes in living cells, fluorescence microscopy represents a tremendous tool in biology. A fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM) has been used recently to monitor protein-DNA associations in plant cells. With this approach, the donor fluorophore is a GFP-tagged binding partner expressed in plant cells. A Sytox® Orange treatment converts nuclear nucleic acids to FRET acceptors. A decrease of GFP lifetime is due to FRET between donor and acceptor, indicating close association of the GFP binding partner and Sytox® Orange-stained DNA. In this chapter, we present a step-by-step protocol for the transient expression in N. benthamiana of GFP-tagged proteins and the fixation and permeabilization procedures used for the preparation of plant material aimed at detecting protein-nucleic acid interactions by FRET-FLIM measurements.
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Affiliation(s)
- Maxime Escouboué
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan, France
| | - Laurent Camborde
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan, France
| | - Alain Jauneau
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan, France
| | - Elodie Gaulin
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan, France
| | - Laurent Deslandes
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan, France.
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52
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Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19061595. [PMID: 29843482 PMCID: PMC6032373 DOI: 10.3390/ijms19061595] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
Intrinsically disordered regions (IDRs) and protein (IDPs) are highly flexible owing to their lack of well-defined structures. A subset of such proteins interacts with various substrates; including RNA; frequently adopting regular structures in the final complex. In this work; we have analysed a dataset of protein–RNA complexes undergoing disorder-to-order transition (DOT) upon binding. We found that DOT regions are generally small in size (less than 3 residues) for RNA binding proteins. Like structured proteins; positively charged residues are found to interact with RNA molecules; indicating the dominance of electrostatic and cation-π interactions. However, a comparison of binding frequency shows that interface hydrophobic and aromatic residues have more interactions in only DOT regions than in a protein. Further; DOT regions have significantly higher exposure to water than their structured counterparts. Interactions of DOT regions with RNA increase the sheet formation with minor changes in helix forming residues. We have computed the interaction energy for amino acids–nucleotide pairs; which showed the preference of His–G; Asn–U and Ser–U at for the interface of DOT regions. This study provides insights to understand protein–RNA interactions and the results could also be used for developing a tool for identifying DOT regions in RNA binding proteins.
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53
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Yu Z, Cowan JA. Metal complexes promoting catalytic cleavage of nucleic acids-biochemical tools and therapeutics. Curr Opin Chem Biol 2018; 43:37-42. [PMID: 29153936 PMCID: PMC5847438 DOI: 10.1016/j.cbpa.2017.10.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/26/2017] [Accepted: 10/29/2017] [Indexed: 01/21/2023]
Abstract
The development of metal complexes that promote degradation of nucleic acids has garnered significant interest as a result of their broad range of potential application. This review focuses on recent progress in the design and synthesis of metal complexes as artificial nucleases that promote either hydrolytic or oxidative cleavage of nucleic acids. Illustrative examples demonstrate the versatility of artificial nucleases for in vitro applications as molecular tools to address biochemical problems, as well as their potential use as therapeutic agents. We also address future challenges for improvement and avenues for further investigation.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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54
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Takakado A, Nakasone Y, Terazima M. Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL222. Biochemistry 2018; 57:1603-1610. [DOI: 10.1021/acs.biochem.7b01206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akira Takakado
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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55
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Affiliation(s)
- Jennie Lin
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
| | - Kiran Musunuru
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
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56
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Abstract
The interaction between a protein and DNA is involved in almost all cellular functions, and is vitally important in transcriptional regulation. There are two complementary approaches used to detect the interactions between a transcription factor (TF) and DNA, i.e., the TF-centered or protein-DNA approach, and the gene-centered or DNA-protein approach. The yeast one-hybrid (Y1H) is a powerful and widely used gene-centered system to identify DNA-protein interactions. However, a powerful and simple TF-centered method to study protein-DNA interactions like Y1H is lacking. Here, we provide a TF-centered method based on the Y1H system to identify the motifs recognized by a defined TF, termed TF-centered Y1H. In this system, a random short DNA sequence insertion library is generated as the prey DNA sequences to interact with a defined TF as the bait. TF-centered Y1H could identify quickly the motifs bound by a defined TF, representing a reliable and efficient approach with the advantages of Y1H. Therefore, this TF-centered Y1H may have a wide application in protein-DNA interaction studies.
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57
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Atomic force spectroscopic and SPR kinetic analysis of long circular and short ssDNA molecules interacting with single-stranded DNA-binding protein. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-2022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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58
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[Letter to the Editor] Incorrect assignment of affected nucleotides in footprinting/probing experiments. Biotechniques 2017; 63:105-106. [PMID: 28911313 DOI: 10.2144/000114585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Sergey Belikov or Lars Wieslander, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden. E-mail: sergey.belikov@su.se or lars.wieslander@su.se.
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59
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WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites. Methods Mol Biol 2017. [PMID: 28842875 DOI: 10.1007/978-1-4939-7098-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We present a method through which one may monitor the relative binding affinity of a given protein to DNA motifs on the scale of a whole genome. Briefly, the protein of interest is incubated with fragmented genomic DNA and then affixed to a column. Washes with buffers containing low salt concentrations will remove nonbound DNA fragments, while stepwise washes with increasing salt concentrations will elute more specifically bound fragments. Massive sequencing is used to identify eluted DNA fragments and map them on the genome, which permits us to classify the different binding sites according to their affinity and determine corresponding consensus motifs (if any).
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60
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Zhang P, Hastert FD, Ludwig AK, Breitwieser K, Hofstätter M, Cardoso MC. DNA base flipping analytical pipeline. Biol Methods Protoc 2017; 2:bpx010. [PMID: 32161792 PMCID: PMC6994035 DOI: 10.1093/biomethods/bpx010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 11/20/2022] Open
Abstract
DNA base modifications and mutations are observed in all genomes throughout the kingdoms of life. Proteins involved in their establishment and removal were shown to use a base flipping mechanism to access their substrates. To better understand how proteins flip DNA bases to modify or remove them, we optimized and developed a pipeline of methods to step-by-step detect the process starting with protein–DNA interaction, base flipping itself and the ensuing DNA base modification or excision. As methylcytosine is the best-studied DNA modification, here we focus on the process of writing, modifying and reading this DNA base. Using multicolor electrophoretic mobility shift assays, we show that the methylcytosine modifier Tet1 exhibits little DNA sequence specificity with only a slight preference for methylated CpG containing DNA. A combination of chloroacetaldehyde treatment and high-resolution melting temperature analysis allowed us to detect base flipping induced by the methylcytosine modifier Tet1 as well as the methylcytosine writer M.HpaII. Finally, we show that high-resolution melting temperature analysis can be used to detect the activity of glycosylases, methyltransferases and dioxigenases on DNA substrates. Taken together, this DNA base flipping analytical pipeline (BaFAP) provide a complete toolbox for the fast and sensitive analysis of proteins that bind, flip and modify or excise DNA bases.
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Affiliation(s)
- Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Kai Breitwieser
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | | | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
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61
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Lu C, Tian S, Zhai G, Yuan Z, Li Y, He X, Zhang Y, Zhang K. Probing the Binding Interfaces of Histone-Aptamer by Photo Cross-Linking Mass Spectrometry. ACS Chem Biol 2017; 12:57-62. [PMID: 27936569 DOI: 10.1021/acschembio.6b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Histone proteins, which could interact with DNA, play important roles in the regulation of chromatin structures, transcription, and other DNA-based biological processes. Here, we developed a novel aptamer-based probe for the analysis of histone H4-aptamer interfaces. This probe contains a DNA sequence for specific recognition of histone H4, a biotin tag for affinity enrichment, an aryl azide photoactive group for cross-linking and a cleavable disulfide group to dissociate aptamer from labeled histones. We successfully achieved specific enrichment of histone H4 and further developed a new analysis strategy for histone-aptamer interaction by photo cross-linking mass spectrometry. The binding area of histone H4 to aptamer was investigated and discussed for the first time. This strategy exhibits great potential and might further contribute to the understanding of histone-DNA interaction patterns.
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Affiliation(s)
- Congcong Lu
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Shanshan Tian
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Guijin Zhai
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Zuofei Yuan
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yijun Li
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Xiwen He
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Yukui Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Kai Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
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62
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Stasyuk OA, Jakubec D, Vondrášek J, Hobza P. Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes. J Chem Theory Comput 2017; 13:877-885. [PMID: 27992205 DOI: 10.1021/acs.jctc.6b00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In view of the importance of protein-DNA interactions in biological processes, we extracted from the Protein Data Bank several one-to-one complexes of amino acids with nucleotides that matched certain geometric and energetic specificity criteria and investigated them using quantum chemistry methods. The CCSD(T)/CBS interaction energies were used as a benchmark to compare the performance of the MP2.5, MP2-F12, DFT-D3, and PM6-D3H4 methods. All methods yielded good agreement with the reference values, with declining accuracy from MP2.5 to PM6-D3H4. Regardless of the site of interaction, the minima found after full optimization in implicit solvent with high dielectric constant were close to the structures experimentally detected in protein-DNA complexes. According to DFT-SAPT analysis, the nature of noncovalent interactions strongly depends on the type of amino acid. The negatively charged sugar-phosphate backbone of DNA heavily influences the strength of interactions and must be included in the computational model, especially in the case of interactions with charged amino acids.
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Affiliation(s)
- Olga A Stasyuk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague , Albertov 6, 128 43 Prague, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic
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63
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Cha YJ, Yoon DK. Control of Periodic Zigzag Structures of DNA by a Simple Shearing Method. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1604247. [PMID: 27862385 DOI: 10.1002/adma.201604247] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/19/2016] [Indexed: 06/06/2023]
Abstract
A periodic zigzag structure of DNA material is successfully fabricated by a simple shearing method. The periodicity of the pattern can be finely controlled by combining the mechanical shearing method with topographic patterns of microchannels. The resultant zigzag patterns can be used as a template to control the alignment of rod-like liquid crystals due to its highly regular periodicity.
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Affiliation(s)
- Yun Jeong Cha
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea
| | - Dong Ki Yoon
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea
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64
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Zhang W, Shi E, Feng Y, Zhao Y, Yang B. Endonuclease-like activity of the N-terminal domain of Euplotes octocarinatus centrin. RSC Adv 2017. [DOI: 10.1039/c7ra07907a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Euplotes octocarinatus centrin (EoCen) is a member of the EF-hand superfamily of calcium-binding proteins, which refer to nucleotide excision repair (NER).
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Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Insitute of Molecular Science
- Taiyuan 030006
- China
| | - Enxian Shi
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Insitute of Molecular Science
- Taiyuan 030006
- China
- Department of Pharmacy
| | - Yanan Feng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Insitute of Molecular Science
- Taiyuan 030006
- China
| | - Yaqin Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Insitute of Molecular Science
- Taiyuan 030006
- China
| | - Binsheng Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education
- Insitute of Molecular Science
- Taiyuan 030006
- China
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65
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Ostatná V, Kasalová-Vargová V, Kékedy-Nagy L, Černocká H, Ferapontova EE. Chronopotentiometric sensing of specific interactions between lysozyme and the DNA aptamer. Bioelectrochemistry 2016; 114:42-47. [PMID: 28063413 DOI: 10.1016/j.bioelechem.2016.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 01/08/2023]
Abstract
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes. Specific lysozyme-DNAapta binding was distinguished from nonspecific lysozyme-DNA interactions at thioglycolic acid-modified mercury electrodes, but not at the dithiothreitol-modified or bare mercury electrodes. Stability of the surface-attached lysozyme-DNAapta layer depended on the stripping current (Istr) intensity, suggesting that the integrity of the layer critically depends on the time of its exposure to negative potentials. Stabilities of different lysozyme-DNA complexes at the negatively polarized electrode surface were tested, and it was shown that structural transitions of the specific lysozyme-DNAapta complexes occur in the Istr ranges different from those observed for assemblies of lysozyme with DNA sequences capable of only nonspecific lysozyme-DNA interactions. Thus, the CPS allows distinct discrimination between specific and non-specific protein-DNA binding and provides valuable information on stability of the nucleic acid-protein interactions at the polarized interfaces.
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Affiliation(s)
- Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.
| | - Veronika Kasalová-Vargová
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
| | - Hana Černocká
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
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66
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A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement. Sci Rep 2016; 6:39653. [PMID: 28008962 PMCID: PMC5180085 DOI: 10.1038/srep39653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022] Open
Abstract
Many fundamental biological processes depend on intricate networks of interactions between proteins and nucleic acids and a quantitative description of these interactions is important for understanding cellular mechanisms governing DNA replication, transcription, or translation. Here we present a versatile method for rapid and quantitative assessment of protein/nucleic acid (NA) interactions. This method is based on protein induced fluorescence enhancement (PIFE), a phenomenon whereby protein binding increases the fluorescence of Cy3-like dyes. PIFE has mainly been used in single molecule studies to detect protein association with DNA or RNA. Here we applied PIFE for steady state quantification of protein/NA interactions by using microwell plate fluorescence readers (mwPIFE). We demonstrate the general applicability of mwPIFE for examining various aspects of protein/DNA interactions with examples from the restriction enzyme BamHI, and the DNA repair complexes Ku and XPF/ERCC1. These include determination of sequence and structure binding specificities, dissociation constants, detection of weak interactions, and the ability of a protein to translocate along DNA. mwPIFE represents an easy and high throughput method that does not require protein labeling and can be applied to a wide range of applications involving protein/NA interactions.
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67
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Sikarwar B, Singh VV, Sharma PK, Kumar A, Thavaselvam D, Boopathi M, Singh B, Jaiswal YK. DNA-probe-target interaction based detection of Brucella melitensis by using surface plasmon resonance. Biosens Bioelectron 2016; 87:964-969. [PMID: 27665519 DOI: 10.1016/j.bios.2016.09.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 12/20/2022]
Abstract
Surface plasmon resonance (SPR) immunosensor using 4-mercaptobenzoic acid (4-MBA) modified gold (4-MBA/Au) SPR chip was developed first time for the detection of Brucella melitensis (B. melitensis) based on the screening of its complementary DNA target by using two different newly designed DNA probes of IS711 gene. Herein, interaction between DNA probes and target molecule are also investigated and result revealed that the interaction is spontaneous. The kinetics and thermodynamic results derived from the experimental data showed that the interaction between complementary DNA targets and probe 1 is more effective than that of probe 2. Equilibrium dissociation constant (KD) and maximum binding capacity of analyte (Bmax) values for the interaction of complementary DNA target with the immobilized DNA probes were calculated by using kinetic evaluation software, and found to be 15.3 pM (KD) and 81.02m° (Bmax) with probe 1 and 54.9pM and 55.29m° (Bmax), respectively. Moreover, real serum samples analysis were also carried out using immobilized probe 1 and probe 2 with SPR which showed the applicability of this methodology and provides an alternative way for the detection of B. melitensis in less than 10min. This remarkable sensing response of present methodology offer a real time and label free detection of biological warfare agent and provide an opportunity to make miniaturized sensor, indicating considerable promise for diverse environmental, bio-defence, clinical diagnostics, food safety, water and security applications.
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Affiliation(s)
- Bhavna Sikarwar
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India
| | - Virendra V Singh
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India
| | - Pushpendra K Sharma
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India
| | - Ashu Kumar
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India
| | | | - Mannan Boopathi
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India.
| | - Beer Singh
- Defence Research and Development Establishment, DRDO, Jhansi Road, Gwalior 474002, India
| | - Yogesh K Jaiswal
- School of Studies in Biochemistry, Jiwaji University, Gwalior 474011, India
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68
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Vickers TA, Crooke ST. Development of a Quantitative BRET Affinity Assay for Nucleic Acid-Protein Interactions. PLoS One 2016; 11:e0161930. [PMID: 27571227 PMCID: PMC5003356 DOI: 10.1371/journal.pone.0161930] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Protein-nucleic acid interactions play a crucial role in the regulation of diverse biological processes. Elucidating the roles that protein-nucleic acid complexes play in the regulation of transcription, translation, DNA replication, repair and recombination, and RNA processing continues to be a crucial aspect of understanding of cell biology and the mechanisms of disease. In addition, proteins have been demonstrated to interact with antisense oligonucleotide therapeutics in a sequence and chemistry dependent manner, influencing ASO potency and distribution in cells and in vivo. While many assays have been developed to measure protein-nucleic acid interactions, many suffer from lack of throughput and sensitivity, or challenges with protein purification and scalability. In this report we present a new BRET assay for the analysis of DNA-protein interactions which makes use of an extremely bright luciferase as a tag for the binding protein, along with a long-wavelength fluorophore conjugated to the nucleic acid. The resulting assay is high throughput, sensitive, does not require protein purification, and even allows for quantitative characterization of these interactions within the biologically relevant context of whole cells.
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Affiliation(s)
- Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
- * E-mail:
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
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69
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Talukder P, Dedkova LM, Ellington AD, Yakovchuk P, Lim J, Anslyn EV, Hecht SM. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins. Bioorg Med Chem 2016; 24:4177-4187. [PMID: 27452282 DOI: 10.1016/j.bmc.2016.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 01/13/2023]
Abstract
Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail.
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Affiliation(s)
- Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew D Ellington
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Petro Yakovchuk
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jaebum Lim
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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70
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Ecco G, Rowe HM, Trono D. A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression. Methods Mol Biol 2016; 1400:403-17. [PMID: 26895067 DOI: 10.1007/978-1-4939-3372-3_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Deposition of epigenetic marks is an important layer of the transcriptional control of retrotransposons, especially during early embryogenesis. Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are one of the largest families of transcription factors, and collectively partake in this process by tethering to thousands of retroelement-containing genomic loci their cofactor KAP1, which acts as a scaffold for a heterochromatin-inducing machinery. However, while the sequence-specific DNA binding potential of the poly-zinc finger-containing KRAB-ZFPs is recognized, very few members of the family have been assigned specific targets. In this chapter, we describe a large-scale functional screen to identify the retroelements bound by individual murine KRAB-ZFPs. Our method is based on the automated transfection of a library of mouse KRAB-ZFP-containing vectors into 293T cells modified to express GFP from a PGK promoter harboring in its immediate vicinity a KAP1-recruiting retroelement-derived sequence. Analysis is then performed by plate reader and flow cytometry fluorescence readout. Such large-scale DNA-centered functional approach can not only help to identify the trans-acting factors responsible for silencing retrotransposons, but also serve as a model for dissecting the transcriptional networks influenced by retroelement-derived cis-acting sequences.
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Affiliation(s)
- Gabriela Ecco
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Helen M Rowe
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Division of Infection and Immunity, Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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71
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Wang X, Xu J, Liu C, Chen Y. Specific interaction of platinated DNA and proteins by surface plasmon resonance imaging. RSC Adv 2016. [DOI: 10.1039/c5ra27719a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A surface plasmon resonance imaging method to differentiate the interaction between the protein human high mobility group box 1 or human nuclear protein positive cofactor 4 (PC4) and DNAs has been developed.
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Affiliation(s)
- Xiao Wang
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Jiying Xu
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Chanjuan Liu
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Yi Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
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73
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Song C, Zhang S, Huang H. Choosing a suitable method for the identification of replication origins in microbial genomes. Front Microbiol 2015; 6:1049. [PMID: 26483774 PMCID: PMC4588119 DOI: 10.3389/fmicb.2015.01049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.
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Affiliation(s)
- Chengcheng Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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74
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Fujii H, Fujita T. Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins. Int J Mol Sci 2015; 16:21802-12. [PMID: 26370991 PMCID: PMC4613281 DOI: 10.3390/ijms160921802] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 08/24/2015] [Accepted: 08/29/2015] [Indexed: 01/06/2023] Open
Abstract
Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions.
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Affiliation(s)
- Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan.
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan.
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75
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Liu Q, Zhang C, Yu L, Shi Y, Zhang L, Peng J, Ji X, Hou M. Study of a humanized inhibitory anti-platelet glycoprotein VI phage antibody from a phage antibody library. ACTA ACUST UNITED AC 2015; 21:60-7. [PMID: 26330203 DOI: 10.1179/1607845415y.0000000047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Objective The aims of the study were to study the effect of anti-platelet glycoprotein (GP) VI auto-antibodies on platelet aggregation and use phage surface display technology to produce anti-platelet GPVI phage antibody fragment, which may be developed to inhibit platelet aggregation in the treatment of cardiovascular disease. Methods Plasma samples from patients with immune thrombocytopenia (ITP) were screened by monoclonal antibody immobilization of the platelet antigen assay and the platelet aggregation test for anti-platelet GPVI auto-antibody with an inhibitory effect. The humanized anti-platelet GPVI phage antibody was produced by phage surface display technology. The function of the phage antibody fragment against platelet aggregation was examined by the platelet aggregation test. Results Of 726 ITP patients, 2 (0.27%) patients' plasma significantly inhibited platelet aggregation induced by collagen-1. After five rounds of selection, enrichment, and purification, a soluble phage antibody fragment was produced, which can inhibit platelet aggregation induced by collagen-1. The results demonstrate that only a few of the screened anti-platelet GPVI auto-antibodies showed an inhibitory effect on platelet aggregation. Discussion A completely humanized anti-GPVI soluble phage antibody can be produced by phage surface display technology. The antibody was able to specifically block collagen-induced platelet aggregation without influencing the aggregation responses to other agonists. Conclusions Results of the present study suggest that very few anti-platelet GPVI auto-antibodies inhibit the aggregation function of platelet. The humanized anti-platelet GPVI produced by phage surface display technology is promising to be used to inhibit platelet aggregation in the treatment of cardiovascular disease.
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Shcherbinin DS, Gnedenko OV, Khmeleva SA, Usanov SA, Gilep AA, Yantsevich AV, Shkel TV, Yushkevich IV, Radko SP, Ivanov AS, Veselovsky AV, Archakov AI. Computer-aided design of aptamers for cytochrome p450. J Struct Biol 2015; 191:112-9. [PMID: 26166326 DOI: 10.1016/j.jsb.2015.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
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Affiliation(s)
- Dmitrii S Shcherbinin
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
| | - Oksana V Gnedenko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Aliaksei V Yantsevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Tatsiana V Shkel
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Ivan V Yushkevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Alexis S Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | | | - Alexander I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
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77
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Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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78
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Ji X, Wang L, Nie X, He L, Zang D, Liu Y, Zhang B, Wang Y. A novel method to identify the DNA motifs recognized by a defined transcription factor. PLANT MOLECULAR BIOLOGY 2014; 86:367-80. [PMID: 25108460 DOI: 10.1007/s11103-014-0234-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 07/29/2014] [Indexed: 05/15/2023]
Abstract
The interaction between a protein and DNA is involved in almost all cellular functions, and is vitally important in cellular processes. Two complementary approaches are used to detect the interactions between a transcription factor (TF) and DNA, i.e. the TF-centered or protein-DNA approach, and the gene-centered or DNA-protein approach. The yeast one-hybrid (Y1H) is a powerful and widely used system to identify DNA-protein interactions. However, a powerful method to study protein-DNA interactions like Y1H is lacking. Here, we developed a protein-DNA method based on the Y1H system to identify the motifs recognized by a defined TF, termed TF-centered Y1H. In this system, a random short DNA sequence insertion library was generated as the prey DNA sequences to interact with a defined TF as the bait. Using this system, novel interactions were detected between DNA motifs and the AtbZIP53 protein from Arabidopsis. We identified six motifs that were specifically bound by AtbZIP53, including five known motifs (DOF, G-box, I-box, BS1 and MY3) and a novel motif BRS1 [basic leucine zipper (bZIP) Recognized Site 1]. The different subfamily bZIP members also recognize these six motifs, further confirming the reliability of the TF-centered Y1H results. Taken together, these results demonstrated that TF-centered Y1H could identify quickly the motifs bound by a defined TF, representing a reliable and efficient approach with the advantages of Y1H. Therefore, this TF-centered Y1H may have a wide application in protein-DNA interaction studies.
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Affiliation(s)
- Xiaoyu Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürūmqi, 830011, Xinjiang, China
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79
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Luo Y, North JA, Poirier MG. Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA. Methods 2014; 70:108-18. [PMID: 25304387 DOI: 10.1016/j.ymeth.2014.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022] Open
Abstract
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodologies that probe both the binding and dissociation kinetics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding the mechanisms by which these complexes function. Here, we describe single-molecule fluorescence methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site within DNA, nucleosomes and nucleosome arrays. This approach allowed for the unexpected observation that nucleosomes impact not only binding but also dissociation kinetics of transcription factors and is well-suited for the investigation of numerous DNA processing complexes that directly interact with DNA organized into chromatin.
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Affiliation(s)
- Yi Luo
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Justin A North
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States.
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80
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Bonvin P, Dunn SM, Rousseau F, Dyer DP, Shaw J, Power CA, Handel TM, Proudfoot AEI. Identification of the pharmacophore of the CC chemokine-binding proteins Evasin-1 and -4 using phage display. J Biol Chem 2014; 289:31846-31855. [PMID: 25266725 DOI: 10.1074/jbc.m114.599233] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To elucidate the ligand-binding surface of the CC chemokine-binding proteins Evasin-1 and Evasin-4, produced by the tick Rhipicephalus sanguineus, we sought to identify the key determinants responsible for their different chemokine selectivities by expressing Evasin mutants using phage display. We first designed alanine mutants based on the Evasin-1·CCL3 complex structure and an in silico model of Evasin-4 bound to CCL3. The mutants were displayed on M13 phage particles, and binding to chemokine was assessed by ELISA. Selected variants were then produced as purified proteins and characterized by surface plasmon resonance analysis and inhibition of chemotaxis. The method was validated by confirming the importance of Phe-14 and Trp-89 to the inhibitory properties of Evasin-1 and led to the identification of a third crucial residue, Asn-88. Two amino acids, Glu-16 and Tyr-19, were identified as key residues for binding and inhibition of Evasin-4. In a parallel approach, we identified one clone (Y28Q/N60D) that showed a clear reduction in binding to CCL3, CCL5, and CCL8. It therefore appears that Evasin-1 and -4 use different pharmacophores to bind CC chemokines, with the principal binding occurring through the C terminus of Evasin-1, but through the N-terminal region of Evasin-4. However, both proteins appear to target chemokine N termini, presumably because these domains are key to receptor signaling. The results also suggest that phage display may offer a useful approach for rapid investigation of the pharmacophores of small inhibitory binding proteins.
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Affiliation(s)
- Pauline Bonvin
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland,; NovImmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland, and
| | - Steven M Dunn
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland
| | - François Rousseau
- NovImmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland, and
| | - Douglas P Dyer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0684
| | - Jeffrey Shaw
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland
| | - Christine A Power
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0684
| | - Amanda E I Proudfoot
- Merck Serono Geneva Research Centre, 9 chemin des Mines, 1202 Geneva, Switzerland,; NovImmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland, and.
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Xu L, Vaidyanathan VG, Cho BP. Real-time surface plasmon resonance study of biomolecular interactions between polymerase and bulky mutagenic DNA lesions. Chem Res Toxicol 2014; 27:1796-807. [PMID: 25195494 PMCID: PMC4203393 DOI: 10.1021/tx500252z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Surface plasmon resonance (SPR) was
used to measure polymerase-binding
interactions of the bulky mutagenic DNA lesions N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl
(FABP) or N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene
(FAAF) in the context of two unique 5′-flanking bases (CG*A and TG*A). The enzymes used
were exo-nuclease-deficient Klenow fragment (Kf-exo–) or polymerase β (pol β). Specific binary and ternary
DNA binding affinities of the enzymes were characterized at subnanomolar
concentrations. The SPR results showed that Kf-exo– binds strongly to a double strand/single strand template/primer
junction, whereas pol β binds preferentially to double-stranded
DNA having a one-nucleotide gap. Both enzymes exhibited tight binding
to native DNA, with high nucleotide selectivity, where the KD values for each base pair increased in the
order dCTP ≪ dTTP ∼ dATP ≪ dGTP. In contrast
to that for pol β, Kf-exo– binds tightly to
lesion-modified templates; however, both polymerases exhibited minimal
nucleotide selectivity toward adducted DNA. Primer steady-state kinetics
and 19F NMR results support the SPR data. The relative
insertion efficiency fins of dCTP opposite
FABP was significantly higher in the TG*A sequence
compared to that in CG*A. Although Kf-exo– was not sensitive to the presence of a DNA lesion,
FAAF-induced conformational heterogeneity perturbed the active site
of pol β, weakening the enzyme’s ability to bind to FAAF
adducts compared to FABP adducts. The present study demonstrates the
effectiveness of SPR for elucidating how lesion-induced conformational
heterogeneity affects the binding capability of polymerases and ultimately
the nucleotide insertion efficiency.
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Affiliation(s)
- Lifang Xu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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Balintová J, Špaček J, Pohl R, Brázdová M, Havran L, Fojta M, Hocek M. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions. Chem Sci 2014; 6:575-587. [PMID: 28970873 PMCID: PMC5618110 DOI: 10.1039/c4sc01906g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/09/2014] [Indexed: 12/17/2022] Open
Abstract
A new azido-based DNA redox label which can be transformed into nitrophenyltriazole by a CuAAC click reaction was developed. It was used for the mapping of DNA–protein interactions with electrochemical detection.
New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA–protein interactions. 5-(4-Azidophenyl)-2′-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2′-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at –0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at –0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA–protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jan Špaček
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Marie Brázdová
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Luděk Havran
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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Ashby J, Schachermeyer S, Duan Y, Jimenez LA, Zhong W. Probing and quantifying DNA–protein interactions with asymmetrical flow field-flow fractionation. J Chromatogr A 2014; 1358:217-24. [DOI: 10.1016/j.chroma.2014.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 12/20/2022]
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84
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Ordinario DD, Burke AM, Phan L, Jocson JM, Wang H, Dickson MN, Gorodetsky AA. Sequence specific detection of restriction enzymes at DNA-modified carbon nanotube field effect transistors. Anal Chem 2014; 86:8628-33. [PMID: 25137193 DOI: 10.1021/ac501441d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein-DNA interactions play a central role in many cellular processes, and their misregulation has been implicated in a number of human diseases. Thus, there is a pressing need for the development of analytical strategies for interrogating the binding of proteins to DNA. Herein, we report the electrical monitoring of a prototypical DNA-binding protein, the PvuII restriction enzyme, at microfluidic-encapsulated, DNA-modified carbon nanotube field effect transistors. Our integrated platform enables the sensitive, sequence specific detection of PvuII at concentrations as low as 0.5 pM in a volume of 0.025 μL (corresponding to ~7500 proteins). These figures of merit compare favorably to state of the art values reported for alternative fluorescent and electrical assays. The overall detection strategy represents a step toward the massively parallel electrical monitoring, identification, and quantification of protein-DNA interactions at arrayed nanoscale devices.
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Affiliation(s)
- David D Ordinario
- Department of Chemical Engineering and Materials Science, University of California, Irvine , Irvine, California 92697, United States
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85
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Monitoring DNA conformation and charge regulations by plasmonic-based electrochemical impedance platform. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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86
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Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014; 30:340-7. [PMID: 24951248 DOI: 10.1016/j.tig.2014.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Abstract
The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly increases the functional diversity of protein species. Predicting functions at the isoform level is essential to further our understanding of developmental abnormalities and cancers, which frequently exhibit aberrant splicing and dysregulation of isoform expression. However, determination of isoform function is very difficult, and efforts to predict isoform function have been limited in the functional genomics field. Deep sequencing of RNA now provides an unprecedented amount of expression data at the transcript level. We describe here emerging computational approaches that integrate such large-scale whole-transcriptome sequencing (RNA-seq) data for predicting the functions of alternatively spliced isoforms, and we discuss their applications in developmental and cancer biology. We outline future directions for isoform function prediction, emphasizing the need for heterogeneous genomic data integration and tissue-specific, dynamic isoform-level network modeling, which will allow the field to realize its full potential.
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Affiliation(s)
- Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA; Department of Electrical Engineering and Computer Science, Ann Arbor, MI, USA.
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87
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Abstract
The yeast one-hybrid (Y1H) system has been among the methods of choice to detect protein-DNA interactions. However, conventional Y1H systems with a single auxotrophic reporter gene often suffer from high incidence of false positives to demonstrate a limited power in large-scale screenings. Here we describe a refined Y1H system that uses two independent bait sequences, each controlling a distinct reporter gene integrated in the host genome. With these modifications and a method of targeted DNA methylation, we succeeded in efficient isolation of clones for methylated DNA-binding proteins from mammalian cDNA libraries.
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88
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Flores JK, Walshe JL, Ataide SF. RNA and RNA–Protein Complex Crystallography and its Challenges. Aust J Chem 2014. [DOI: 10.1071/ch14319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA biology has changed completely in the past decade with the discovery of non-coding RNAs. Unfortunately, obtaining mechanistic information about these RNAs alone or in cellular complexes with proteins has been a major problem. X-ray crystallography of RNA and RNA–protein complexes has suffered from the major problems encountered in preparing and purifying them in large quantity. Here, we review the available techniques and methods in vitro and in vivo used to prepare and purify RNA and RNA–protein complex for crystallographic studies. We also discuss the future directions necessary to explore the vast number of RNA species waiting for their atomic-resolution structure to be determined.
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89
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Brand LH, Henneges C, Schüssler A, Kolukisaoglu HÜ, Koch G, Wallmeroth N, Hecker A, Thurow K, Zell A, Harter K, Wanke D. Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA. PLoS One 2013; 8:e75177. [PMID: 24146751 PMCID: PMC3795721 DOI: 10.1371/journal.pone.0075177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/12/2013] [Indexed: 12/22/2022] Open
Abstract
DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA. Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed. Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation. To close this gap, we report an automatable DNA-protein-interaction (DPI)-ELISA screen of an optimized double-stranded DNA (dsDNA) probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs. In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation. Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus. We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP. As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences. In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi. Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1. A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding. This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts. Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a deeper understanding of gene regulation in any organism of choice.
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Affiliation(s)
- Luise H. Brand
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
| | - Carsten Henneges
- Cognitive Systems, Center for Bioinformatics, University of Tuebingen, Tuebingen, Germany
| | - Axel Schüssler
- Cognitive Systems, Center for Bioinformatics, University of Tuebingen, Tuebingen, Germany
| | - H. Üner Kolukisaoglu
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
- Center for Life Science Automation, Rostock, Germany
| | - Grit Koch
- Center for Life Science Automation, Rostock, Germany
| | - Niklas Wallmeroth
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
| | - Andreas Hecker
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Andreas Zell
- Cognitive Systems, Center for Bioinformatics, University of Tuebingen, Tuebingen, Germany
| | - Klaus Harter
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
| | - Dierk Wanke
- Plant Physiology, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, Germany
- * E-mail:
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90
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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91
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Winterbach W, Mieghem PV, Reinders M, Wang H, Ridder DD. Topology of molecular interaction networks. BMC SYSTEMS BIOLOGY 2013; 7:90. [PMID: 24041013 PMCID: PMC4231395 DOI: 10.1186/1752-0509-7-90] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/01/2013] [Indexed: 12/23/2022]
Abstract
Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.
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Affiliation(s)
- Wynand Winterbach
- Network Architectures and Services, Department of Intelligent Systems, Faculty of
Electrical Engineering, Mathematics and Computer Science, Delft University of
Technology, P.O. Box 5031, 2600 GA Delft, The Netherlands
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty of Electrical
Engineering, Mathematics and Computer Science, Delft University of Technology,
P.O. Box 5031, 2600 GA Delft, The Netherlands
| | - Piet Van Mieghem
- Network Architectures and Services, Department of Intelligent Systems, Faculty of
Electrical Engineering, Mathematics and Computer Science, Delft University of
Technology, P.O. Box 5031, 2600 GA Delft, The Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty of Electrical
Engineering, Mathematics and Computer Science, Delft University of Technology,
P.O. Box 5031, 2600 GA Delft, The Netherlands
- Netherlands Bioinformatics Center, 6500 HB Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, 2600 GA Delft, The
Netherlands
| | - Huijuan Wang
- Network Architectures and Services, Department of Intelligent Systems, Faculty of
Electrical Engineering, Mathematics and Computer Science, Delft University of
Technology, P.O. Box 5031, 2600 GA Delft, The Netherlands
| | - Dick de Ridder
- Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty of Electrical
Engineering, Mathematics and Computer Science, Delft University of Technology,
P.O. Box 5031, 2600 GA Delft, The Netherlands
- Netherlands Bioinformatics Center, 6500 HB Nijmegen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, 2600 GA Delft, The
Netherlands
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92
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Dendrimer functionalization of gold surface improves the measurement of protein–DNA interactions by surface plasmon resonance imaging. Biosens Bioelectron 2013; 43:148-54. [DOI: 10.1016/j.bios.2012.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 01/05/2023]
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93
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Sobolčiak P, Špírek M, Katrlík J, Gemeiner P, Lacík I, Kasák P. Light-Switchable Polymer from Cationic to Zwitterionic Form: Synthesis, Characterization, and Interactions with DNA and Bacterial Cells. Macromol Rapid Commun 2013; 34:635-9. [DOI: 10.1002/marc.201200823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/21/2013] [Indexed: 11/06/2022]
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94
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Zheng L, Li D, Xiang X, Tong L, Qi M, Pu J, Huang K, Tong Q. Methyl jasmonate abolishes the migration, invasion and angiogenesis of gastric cancer cells through down-regulation of matrix metalloproteinase 14. BMC Cancer 2013; 13:74. [PMID: 23394613 PMCID: PMC3576238 DOI: 10.1186/1471-2407-13-74] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/30/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Recent evidence indicates that methyl jasmonate (MJ), a plant stress hormone, exhibits anti-cancer activity on human cancer cells. The aim of this study is to determine whether sub-cytotoxic MJ can abolish the migration, invasion and angiogenesis gastric cancer cells. METHODS Human gastric cancer cell lines SGC-7901 and MKN-45 were treated with diverse concentrations of MJ. Cell viability, proliferation, migration, invasion and angiogenesis capabilities of cancer cells were measured by MTT colorimetry, EdU incorporation, scratch assay, matrigel invasion assay, and tube formation assay. Gene expression was detected by western blot and real-time quantitative RT-PCR. Binding of transcription factor on gene promoter was detected by chromatin immunoprecipitation. RESULTS Sub-cytotoxic (0.05 to 0.2 mM) MJ attenuated the migration, invasion and angiogenesis, but not the cell viability or proliferation, of gastric cancer cells in a time- and dose-dependent manner, with down-regulation of matrix metalloproteinase 14 (MMP-14) and its downstream gene vascular endothelial growth factor. Restoration of MMP-14 expression rescued the SGC-7901 and MKN-45 cells from sub-cytotoxic MJ-inhibited migration, invasion and angiogenesis. In addition, sub-cytotoxic MJ decreased the specificity protein 1 (Sp1) expression and binding on MMP-14 promoter, while restoration of Sp1 expression rescued the cancer cells from sub-cytotoxic MJ-mediated defects in MMP-14 expression, migration, invasion and angiogenesis. CONCLUSIONS Sub-cytotoxic MJ attenuates the MMP-14 expression via decreasing the Sp1 expression and binding on MMP-14 promoter, thus inhibiting the migration, invasion and angiogenesis of gastric cancer cells.
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Affiliation(s)
- Liduan Zheng
- Department of Pathology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430022, People’s Republic of China
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95
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Locus-specific biochemical epigenetics/chromatin biochemistry by insertional chromatin immunoprecipitation. ISRN BIOCHEMISTRY 2013; 2013:913273. [PMID: 25969763 PMCID: PMC4392943 DOI: 10.1155/2013/913273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 11/27/2012] [Indexed: 11/17/2022]
Abstract
Comprehensive understanding of regulation mechanisms of biological phenomena mediated by functions of genomic DNA requires identification of molecules bound to genomic regions of interest in vivo. However, nonbiased methods to identify molecules bound to specific genomic loci in vivo are limited. To perform biochemical and molecular biological analysis of specific genomic regions, we developed the insertional chromatin immunoprecipitation (iChIP) technology to purify the genomic regions of interest. We applied iChIP to direct identification of components of insulator complexes, which function as boundaries of chromatin domain, showing that it is feasible to directly identify proteins and RNA bound to a specific genomic region in vivo by using iChIP. In addition, recently, we succeeded in identifying proteins and genomic regions interacting with a single copy endogenous locus. In this paper, we will discuss the application of iChIP to epigenetics and chromatin research.
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96
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Abstract
The band-shift assay using polyacrylamide gel electrophoresis is a powerful technique used to investigate DNA-protein interactions. The basis of the method is the separation of free DNA from DNA-protein complexes by virtue of differences in charge, size, and shape. The band-shift assay can be used to determine thermodynamic and kinetic binding constants and also to analyze the composition and stoichiometries of DNA-protein complexes.
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Affiliation(s)
- Lynn Powell
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
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97
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Reece-Hoyes JS, Marian Walhout AJ. Yeast one-hybrid assays: a historical and technical perspective. Methods 2012; 57:441-7. [PMID: 22884952 DOI: 10.1016/j.ymeth.2012.07.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 07/25/2012] [Accepted: 07/27/2012] [Indexed: 01/07/2023] Open
Abstract
Since its development about two decades ago, the yeast one-hybrid (Y1H) assay has become an important technique for detecting physical interactions between sequence-specific regulatory transcription factor proteins (TFs) and their DNA target sites. Multiple versions of the Y1H methodology have been developed, each with technical differences and unique advantages. We will discuss several of these technical variations in detail, and also provide some ideas for how Y1H assays can be further improved.
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Affiliation(s)
- John S Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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98
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Vaidyanathan VG, Xu L, Cho BP. Binary and ternary binding affinities between exonuclease-deficient Klenow fragment (Kf-exo(-)) and various arylamine DNA lesions characterized by surface plasmon resonance. Chem Res Toxicol 2012; 25:1568-70. [PMID: 22804627 DOI: 10.1021/tx300289d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We used surface plasmon resonance (SPR) to characterize the binding interactions between the exonulease-free Klenow fragment (Kf-exo(-)) and unmodified and modified dG adducts derived from arylamine carcinogens: fluorinated 2-aminofluorene (FAF), 2-acetylaminofluorene (FAAF), and 4-aminobiphenyl (FABP). Tight polymerase binding was detected with unmodified dG and the correct dCTP. The discrimination of correct versus incorrect nucleotides was pronounced with K(D) values in the order of dCTP ≪ dTTP < dATP < dGTP. In contrast, minimal selectivity was observed for the modified templates with Kf-exo(-) binding tighter to the FAAF (k(off): 0.02 s(-1)) and FABP (k(off): 0.01 s(-1)) lesions than to FAF (k(off): 0.04 s(-1)).
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Affiliation(s)
- V G Vaidyanathan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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