1
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Jin S, Li D, Feng X, Fu G. Synthesis of carbon dots-based surface protein-imprinted nanoparticles via sandwich-structured template pre-assemble and post-imprinting modification for enhanced fluorescence detection. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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3
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Lai SM, Gopalan V. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs. Methods Mol Biol 2021; 2167:147-169. [PMID: 32712919 DOI: 10.1007/978-1-0716-0716-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kink-turns are important RNA structural modules that facilitate long-range tertiary interactions and form binding sites for members of the L7Ae family of proteins. Present in a wide variety of functional RNAs, kink-turns play key organizational roles in many RNA-based cellular processes, including translation, modification, and tRNA biogenesis. It is important to determine the contribution of kink-turns to the overall architecture of resident RNAs, as these modules dictate ribonucleoprotein (RNP) assembly and function. This chapter describes a site-directed, hydroxyl radical-mediated footprinting strategy that utilizes L7Ae-tethered chemical nucleases to experimentally validate computationally identified kink-turns in any RNA and under a wide variety of conditions. The work plan described here uses the catalytic RNase P RNA as an example to provide a blueprint for using this footprinting method to map RNA-protein interactions in other RNP complexes.
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Affiliation(s)
- Stella M Lai
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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4
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Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
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Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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5
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Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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6
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Ghorbani M, Mahmoodzadeh F, Nezhad-Mokhtari P, Hamishehkar H. A novel polymeric micelle-decorated Fe3O4/Au core–shell nanoparticle for pH and reduction-responsive intracellular co-delivery of doxorubicin and 6-mercaptopurine. NEW J CHEM 2018. [DOI: 10.1039/c8nj03310b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synergistic antitumor activity against MCF-7 cells was confirmed by co-delivery of doxorubicin and 6-mercaptopurine via dual pH/reduction-responsive nanoparticles.
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Affiliation(s)
- Marjan Ghorbani
- Stem Cell Research Center
- Tabriz University of Medical Sciences
- Tabriz
- Iran
| | | | | | - Hamed Hamishehkar
- Drug Applied Research Center
- Tabriz University of Medical Sciences
- Tabriz
- Iran
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7
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Yuan Q, Kong XT, Hou GL, Jiang L, Wang XB. Photoelectron spectroscopic and computational studies of [EDTA·M(iii)]− complexes (M = H3, Al, Sc, V–Co). Phys Chem Chem Phys 2018; 20:19458-19469. [DOI: 10.1039/c8cp01548a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectron spectroscopic and computational studies of [EDTA·M(iii)]− complexes reveal their redox chemistry and specific metal bindings.
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Affiliation(s)
- Qinqin Yuan
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Xiang-Tao Kong
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Gao-Lei Hou
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Xue-Bin Wang
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
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8
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Ghorbani M, Hamishehkar H. Decoration of gold nanoparticles with thiolated pH-responsive polymeric (PEG-b-p(2-dimethylamio ethyl methacrylate-co-itaconic acid) shell: A novel platform for targeting of anticancer agent. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 81:561-570. [DOI: 10.1016/j.msec.2017.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/24/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
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9
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Voong LN, Xi L, Wang JP, Wang X. Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping. Trends Genet 2017; 33:495-507. [PMID: 28693826 DOI: 10.1016/j.tig.2017.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/10/2017] [Accepted: 05/30/2017] [Indexed: 12/30/2022]
Abstract
Nucleosomes regulate the transcription output of the genome by occluding the underlying DNA sequences from DNA-binding proteins that must act on it. Knowledge of the precise locations of nucleosomes in the genome is thus essential towards understanding how transcription is regulated. Current nucleosome-mapping strategies involve digesting chromatin with nucleases or chemical cleavage followed by high-throughput sequencing. In this review, we compare the traditional micrococcal nuclease (MNase)-based approach with a chemical cleavage strategy, with discussion on the important insights each has uncovered about the role of nucleosomes in shaping transcriptional processes.
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Affiliation(s)
- Lilien N Voong
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Liqun Xi
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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10
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Redox and pH-responsive gold nanoparticles as a new platform for simultaneous triple anti-cancer drugs targeting. Int J Pharm 2017; 520:126-138. [DOI: 10.1016/j.ijpharm.2017.02.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/26/2017] [Accepted: 02/01/2017] [Indexed: 12/12/2022]
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11
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Ghorbani M, Hamishehkar H, Hajipour H, Arsalani N, Entezami AA. Ternary-responsive magnetic nanocarriers for targeted delivery of thiol-containing anticancer drugs. NEW J CHEM 2016. [DOI: 10.1039/c5nj03602j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cancer is currently the second leading cause of death in the world and one of the most serious challenges in medical therapy.
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Affiliation(s)
- Marjan Ghorbani
- Laboratory of Polymer
- Faculty of Chemistry
- University of Tabriz
- Tabriz
- Iran
| | - Hamed Hamishehkar
- Drug Applied Research Center
- Tabriz University of Medical Sciences
- Tabriz
- Iran
| | - Hamed Hajipour
- Biotechnology Research Center
- Tabriz University of Medical Sciences
- Tabriz
- Iran
| | - Naser Arsalani
- Laboratory of Polymer
- Faculty of Chemistry
- University of Tabriz
- Tabriz
- Iran
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12
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Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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13
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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14
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Cunningham TF, Shannon MD, Putterman MR, Arachchige RJ, Sengupta I, Gao M, Jaroniec CP, Saxena S. Cysteine-specific Cu2+ chelating tags used as paramagnetic probes in double electron electron resonance. J Phys Chem B 2015; 119:2839-43. [PMID: 25608028 DOI: 10.1021/jp5103143] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double electron electron resonance (DEER) is an attractive technique that is utilized for gaining insight into protein structure and dynamics via nanometer-scale distance measurements. The most commonly used paramagnetic tag in these measurements is a nitroxide spin label, R1. Here, we present the application of two types of high-affinity Cu(2+) chelating tags, based on the EDTA and cyclen metal-binding motifs as alternative X-band DEER probes, using the B1 immunoglobulin-binding domain of protein G (GB1) as a model system. Both types of tags have been incorporated into a variety of protein secondary structure environments and exhibit high spectral sensitivity. In particular, the cyclen-based tag displays distance distributions with comparable distribution widths and most probable distances within 1-3 Å when compared to homologous R1 distributions. The results display the viability of the cyclen tag as an alternative to the R1 side chain for X-band DEER distance measurements in proteins.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh , 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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15
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Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation. Methods Mol Biol 2015; 1276:101-31. [PMID: 25665560 PMCID: PMC4677679 DOI: 10.1007/978-1-4939-2392-2_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A three-step procedure comprising (1) unnatural-amino-acid mutagenesis with 4-azido-phenylalanine, (2) Staudinger-Bertozzi ligation with a probe-phosphine derivative, and (3) in vitro reconstitution of RNA polymerase (RNAP) enables the efficient site-specific incorporation of a fluorescent probe, a spin label, a cross-linking agent, a cleaving agent, an affinity tag, or any other biochemical or biophysical probe, at any site of interest in RNAP. Straightforward extensions of the procedure enable the efficient site-specific incorporation of two or more different probes in two or more different subunits of RNAP. We present protocols for synthesis of probe-phosphine derivatives, preparation of RNAP subunits and the transcription initiation factor σ, unnatural amino acid mutagenesis of RNAP subunits and σ, Staudinger ligation with unnatural-amino-acid-containing RNAP subunits and σ, quantitation of labelling efficiency and labelling specificity, and reconstitution of RNAP.
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16
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Sengupta I, Gao M, Arachchige RJ, Nadaud PS, Cunningham TF, Saxena S, Schwieters CD, Jaroniec CP. Protein structural studies by paramagnetic solid-state NMR spectroscopy aided by a compact cyclen-type Cu(II) binding tag. JOURNAL OF BIOMOLECULAR NMR 2015; 61:1-6. [PMID: 25432438 PMCID: PMC4304965 DOI: 10.1007/s10858-014-9880-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 05/07/2023]
Abstract
Paramagnetic relaxation enhancements (PREs) are a rich source of structural information in protein solid-state NMR spectroscopy. Here we demonstrate that PRE measurements in natively diamagnetic proteins are facilitated by a thiol-reactive compact, cyclen-based, high-affinity Cu(2+) binding tag, 1-[2-(pyridin-2-yldisulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (TETAC), that overcomes the key shortcomings associated with the use of larger, more flexible metal-binding tags. Using the TETAC-Cu(2+) K28C mutant of B1 immunoglobulin-binding domain of protein G as a model, we find that amino acid residues located within ~10 Å of the Cu(2+) center experience considerable transverse PREs leading to severely attenuated resonances in 2D (15)N-(13)C correlation spectra. For more distant residues, electron-nucleus distances are accessible via quantitative measurements of longitudinal PREs, and we demonstrate such measurements for (15)N-Cu(2+) distances up to ~20 Å.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Min Gao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rajith J. Arachchige
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Timothy F. Cunningham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Charles D. Schwieters
- Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding author: Christopher P. Jaroniec,
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17
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Polymer conjugates of doxorubicin bound through an amide and hydrazone bond: Impact of the carrier structure onto synergistic action in the treatment of solid tumours. Eur J Pharm Sci 2014; 58:1-12. [DOI: 10.1016/j.ejps.2014.02.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 11/23/2022]
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18
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Sengupta I, Nadaud PS, Jaroniec CP. Protein structure determination with paramagnetic solid-state NMR spectroscopy. Acc Chem Res 2013; 46:2117-26. [PMID: 23464364 DOI: 10.1021/ar300360q] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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19
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Novo L, van Gaal EVB, Mastrobattista E, van Nostrum CF, Hennink WE. Decationized crosslinked polyplexes for redox-triggered gene delivery. J Control Release 2013; 169:246-56. [PMID: 23583705 DOI: 10.1016/j.jconrel.2013.03.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 11/16/2022]
Abstract
The clinical applicability of polymers as gene delivery systems depends not only on their efficiency, but also on their safety. The cytotoxicity of these systems remains a major issue, mainly due to their cationic nature. Therefore, it is highly preferable to have a system based on biocompatible neutral polymers, lacking polycations, without compromising the DNA condensing and protecting capacities. Here, we introduce a concept to obtain a neutral polymeric gene delivery system, through a 3-step process (charge-driven condensation; stabilization through disulfide crosslinking; polyplex decationization) to generate polyplexes with a core of disulfide crosslinked poly(hydroxypropyl methacrylamide) (pHPMA) in which plasmid DNA (pDNA) is entrapped and a shell of poly(ethylene glycol) (PEG). The resulting polyplexes combine beneficial features of high and stable DNA loading capacity, stealth behavior and reduced toxicity. The nanoparticles are designed to release the pDNA after cellular uptake through cleavage of disulfide crosslinks within the intracellular reducing environment. This was shown by forced introduction of the polyplexes into the cytosol of HeLa cells by electroporation, which resulted in a high level of expression of the reporter gene. Additionally, the decationized polyplexes showed no interference on the cellular cell viability or metabolic activity (even at high dose) and no complex-induced membrane destabilization. Furthermore, decationized polyplexes showed a low degree of non-specific uptake, which is a highly favorable property for targeted therapy. Summarizing, the stabilized, decationized polyplexes presented here contribute to solve the high toxicity, low stability and lack of cellular/tissue specificity of cationic polymer based gene delivery systems.
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Affiliation(s)
- Luís Novo
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
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20
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Zhang X, Du F, Huang J, Lu W, Liu S, Yu J. Fabrication of biodegradable micelles with reduction-triggered release of 6-mercaptopurine profile based on disulfide-linked graft copolymer conjugate. Colloids Surf B Biointerfaces 2012; 100:155-62. [DOI: 10.1016/j.colsurfb.2012.04.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 04/17/2012] [Accepted: 04/19/2012] [Indexed: 11/17/2022]
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Muthukrishnan N, Johnson GA, Lim J, Simanek EE, Pellois JP. TAT-mediated photochemical internalization results in cell killing by causing the release of calcium into the cytosol of cells. Biochim Biophys Acta Gen Subj 2012; 1820:1734-43. [PMID: 22771830 DOI: 10.1016/j.bbagen.2012.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/06/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lysis of endocytic organelles is a necessary step in many cellular delivery methodologies. This is achieved efficiently in the photochemical internalization approach but the cell death that accompanies this process remains a problem. METHODS We investigate the mechanisms of cell death that accompanies photochemical internalization of the fluorescent peptide TMR-TAT. RESULTS TMR-TAT kills cells after endocytosis and light irradiation. The lysis of endocytic organelles by TMR-TAT causes a rapid increase in the concentration of calcium in the cytosol. TMR-TAT co-localizes with endocytic organelles containing calcium prior to irradiation and photochemical internalization leads to the release of the lumenal content of these organelles. Ruthenium red and cyclosporin A, inhibitors of calcium import in mitochondria and of the mitochondria permeability transition pore, inhibit cell death. CONCLUSIONS TMR-TAT mediated photochemical internalization leads to a disruption of calcium homeostasis. The subsequent import of calcium in mitochondria is a causative factor of the cell death that accompanies photochemical internalization. General significance Understanding how the lysis of endocytic organelles affects cellular physiology and causes cell death is crucial to the development of optimal delivery methodologies.
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Affiliation(s)
- Nandhini Muthukrishnan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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22
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Jin HJ, Lu J, Wu X. Development of a new enzyme-responsive self-immolative spacer conjugate applicable to the controlled drug release. Bioorg Med Chem 2012; 20:3465-9. [DOI: 10.1016/j.bmc.2012.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/04/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
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23
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Jaroniec CP. Solid-state nuclear magnetic resonance structural studies of proteins using paramagnetic probes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 43-44:1-13. [PMID: 22464402 DOI: 10.1016/j.ssnmr.2012.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/31/2023]
Abstract
Determination of three-dimensional structures of biological macromolecules by magic-angle spinning (MAS) solid-state NMR spectroscopy is hindered by the paucity of nuclear dipolar coupling-based restraints corresponding to distances exceeding 5 Å. Recent MAS NMR studies of uniformly (13)C,(15)N-enriched proteins containing paramagnetic centers have demonstrated the measurements of site-specific nuclear pseudocontact shifts and spin relaxation enhancements, which report on electron-nucleus distances up to ~20 Å. These studies pave the way for the application of such long-distance paramagnetic restraints to protein structure elucidation and analysis of protein-protein and protein-ligand interactions in the solid phase. Paramagnetic species also facilitate the rapid acquisition of high resolution and sensitivity multidimensional solid-state NMR spectra of biomacromolecules using condensed data collection schemes, and characterization of solvent-accessible surfaces of peptides and proteins. In this review we discuss some of the latest applications of magic-angle spinning NMR spectroscopy in conjunction with paramagnetic probes to the structural studies of proteins in the solid state.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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Orientation of Pseudomonas aeruginosa ExsA monomers bound to promoter DNA and base-specific contacts with the P(exoT) promoter. J Bacteriol 2012; 194:2573-85. [PMID: 22408167 DOI: 10.1128/jb.00107-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ExsA is a transcriptional activator of the Pseudomonas aeruginosa type III secretion system (T3SS) and a member of the AraC/XylS protein family. Each of the 10 ExsA-dependent promoter regions that define the T3SS regulon has two adjacent binding sites for monomeric ExsA. Whereas the promoter-proximal sites (binding site 1) contain highly conserved GnC and TGnnA sequences that are separated by ∼10 bp, the promoter-distal sites (binding site 2) share no obvious sequence similarity to each other or to the binding site 1 consensus. In the present study, we used footprinting with Fe-BABE (a protein-labeling reagent that can be conjugated to cysteine residues) to demonstrate that the two ExsA monomers bind to the P(exsC), P(exsD), P(exoT), and P(pcrG) promoters in a head-to-tail orientation. The footprinting data further indicate that the conserved GnC and TGnnA sequences constitute binding site 1. When bound to site 1, the first helix-turn-helix (HTH) motif of ExsA interacts with the conserved GnC sequence, and the second HTH interacts at or near the TGnnA sequences. Genetic data using the P(exoT) promoter indicate that residues L198 and T199 in the first HTH motif of ExsA contact the guanine in the GnC sequence and that residue K202, also in the first HTH motif, contacts the cytosine. Likewise, evidence is presented that residues Q248, Y250, T252, and R257 located in the second HTH motif contribute to the recognition of the TGnnA sequence. These combined data define interactions of ExsA with site 1 on the P(exoT) promoter and provide insight into the nature of the interactions involved in recognition of binding site 2.
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25
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Nadaud PS, Sengupta I, Helmus JJ, Jaroniec CP. Evaluation of the influence of intermolecular electron-nucleus couplings and intrinsic metal binding sites on the measurement of 15N longitudinal paramagnetic relaxation enhancements in proteins by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:293-302. [PMID: 21826518 DOI: 10.1007/s10858-011-9536-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
Magic-angle spinning solid-state NMR measurements of (15)N longitudinal paramagnetic relaxation enhancements (PREs) in (13)C,(15)N-labeled proteins modified with Cu(2+)-chelating tags can yield multiple long-range electron-nucleus distance restraints up to ~20 Å (Nadaud et al. in J Am Chem Soc 131:8108-8120, 2009). Using the EDTA-Cu(2+) K28C mutant of B1 immunoglobulin binding domain of protein G (GB1) as a model, we investigate the effects on such measurements of intermolecular electron-nucleus couplings and intrinsic metal binding sites, both of which may potentially complicate the interpretation of PRE data in terms of the intramolecular protein fold. To quantitatively assess the influence of intermolecular (15)N-Cu(2+) interactions we have determined a nearly complete set of longitudinal (15)N PREs for a series of microcrystalline samples containing ~10, 15 and 25 mol percent of the (13)C,(15)N-labeled EDTA-Cu(2+)-tagged protein diluted in a matrix of diamagnetic natural abundance GB1. The residual intermolecular interactions were found to be minor on the whole and account for only a fraction of the relatively small but systematic deviations observed between the experimental (15)N PREs and corresponding values calculated using protein structural models for residues furthest removed from the EDTA-Cu(2+) tag. This suggests that these deviations are also caused in part by other factors not related to the protein structure, such as the presence in the protein of intrinsic secondary sites capable of binding Cu(2+) ions. To probe this issue we performed a Cu(2+) titration study for K28C-EDTA GB1 monitored by 2D (15)N-(1)H solution-state NMR, which revealed that while for Cu(2+):protein molar ratios of ≤ 1.0 Cu(2+) binds primarily to the high-affinity EDTA tag, as anticipated, at even slightly super-stoichiometric ratios the Cu(2+) ions can also associate with side-chains of aspartate and glutamate residues. This in turn is expected to lead to enhanced PREs for residues located in the vicinity of the secondary Cu(2+) binding sites, and indeed many of these residues were ones found to display the elevated longitudinal (15)N PREs in the solid phase.
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Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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26
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Flaus A. Principles and practice of nucleosome positioningin vitro. FRONTIERS IN LIFE SCIENCE 2011. [DOI: 10.1080/21553769.2012.702667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Kasianowicz J, Walker B, Krishnasastry M, Bayley H. Genetically Engineered Pores as Metal Ion Biosensors. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-330-217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTWe are adapting proteins that form pores in lipid bilayers for use as components of biosensors. Specifically, we have produced genetically engineered variants of the α hemolysin (αHL) fromStaphylococcusaureus with properties that are sensitive to low concentrations of divalent cations. For example, the pore-forming activity of one mutant (αHL-H5: residues 130–134 inclusive replaced with histidine) is inhibited by Zn2+at concentrations as low as 1 μM, as judged by the reduction in its ability to lyse rabbit red blood cells and to increase the conductance of planar lipid bilayer membranes. When αHL-H5 is added to the aqueous phase bathing one side of a planar membrane, the subsequent addition of 100 μM Zn2+to either side blocks the pores that form. This result suggests that at least part of the mutated region lines the channel lumen. Ca2+and Mg2+do not block the channel and therefore the H5 mutation confers a degree of analyte specificity to the αHL pore. The results suggest that genetically engineered pores have great promise for the rapid and sensitive detection of metal cations and we discuss the merits and potential limitations for their use in this application. Specifically, we examine the issues of selectivity, sensitivity, response time, dynamic range and longevity. Some of these properties are interdependent. For example, the goals of high sensitivity and rapid response time can be in conflict.
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28
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Etrych T, Kovář L, Šubr V, Braunová A, Pechar M, Chytil P, Říhova B, Ulbrich K. High-molecular-weight Polymers Containing Biodegradable Disulfide Bonds: Synthesis and In Vitro Verification of Intracellular Degradation. J BIOACT COMPAT POL 2010. [DOI: 10.1177/0883911509353485] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The synthesis, physico-chemical behavior, and in vitro intracellular degradation of new biodegradable graft, diblock or multiblock polymer carriers that were designed to deliver bioactive compounds by passive tumor targeting were investigated. The graft polymer carriers consisted of the N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer backbone grafted with a semitelechelic HPMA copolymer. The diblock polymer carriers were prepared by condensation of two semitelechelic HPMA copolymers. The multiblock polymer drug carrier was prepared by oxidative polycondensation of PEG-bis-cysteine. In all three carrier systems, the single polymers were linked via biodegradable disulfide bonds forming the graft, diblock or multiblock polymers. These polymers are potential polymer carriers for solid tumor-specific drug delivery with subsequent intracellular degradation to short polymer fragments that can be excreted by glomerular filtration. Prolonged blood circulation, accumulation in solid tumors, and drug release from these carriers have been reported. Here, degradation of the polymers in model buffer solutions mimicking intracellular environment as well as after incubation with EL4 T-cell lymphoma cancer cells were investigated. In both cases, degradation resulted in polymer fragments of molecular weight below the renal threshold.
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Affiliation(s)
- Tomáš Etrych
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic,
| | - Lubomír Kovář
- Institute of Microbiology, Academy of Sciences of the Czech Republic Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Šubr
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Alena Braunová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Michal Pechar
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Petr Chytil
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Blanka Říhova
- Institute of Microbiology, Academy of Sciences of the Czech Republic Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Karel Ulbrich
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
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29
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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30
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Schirle NT, Goodman RA, Krishnamurthy M, Beal PA. Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide. Org Biomol Chem 2010; 8:4898-904. [DOI: 10.1039/c0ob00309c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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31
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Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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32
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Nadaud PS, Helmus JJ, Kall SL, Jaroniec CP. Paramagnetic Ions Enable Tuning of Nuclear Relaxation Rates and Provide Long-Range Structural Restraints in Solid-State NMR of Proteins. J Am Chem Soc 2009; 131:8108-20. [DOI: 10.1021/ja900224z] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S. Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Jonathan J. Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Stefanie L. Kall
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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33
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Zhu Y, Wang Y, Chen G. Molecular Dynamics Simulations on Binding Models of Dervan-Type Polyamide + Cu(II) Nuclease Ligands to DNA. J Phys Chem B 2008; 113:839-48. [DOI: 10.1021/jp8091545] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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34
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Ossipov DA, Piskounova S, Hilborn J. Poly(vinyl alcohol) Cross-Linkers for in Vivo Injectable Hydrogels. Macromolecules 2008. [DOI: 10.1021/ma800332c] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitri A. Ossipov
- Polymer Chemistry, Material Chemistry Department, Uppsala University, S-75121 Uppsala, Sweden
| | - Sonya Piskounova
- Polymer Chemistry, Material Chemistry Department, Uppsala University, S-75121 Uppsala, Sweden
| | - Jöns Hilborn
- Polymer Chemistry, Material Chemistry Department, Uppsala University, S-75121 Uppsala, Sweden
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35
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Iwahara J, Tang C, Marius Clore G. Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:185-95. [PMID: 17084097 PMCID: PMC1994582 DOI: 10.1016/j.jmr.2006.10.003] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/06/2006] [Accepted: 10/16/2006] [Indexed: 05/05/2023]
Abstract
The use of (1)H transverse paramagnetic relaxation enhancement (PRE) has seen a resurgence in recent years as method for providing long-range distance information for structural studies and as a probe of large amplitude motions and lowly populated transient intermediates in macromolecular association. In this paper we discuss various practical aspects pertaining to accurate measurement of PRE (1)H transverse relaxation rates (Gamma(2)). We first show that accurate Gamma(2) rates can be obtained from a two time-point measurement without requiring any fitting procedures or complicated error estimations, and no additional accuracy is achieved from multiple time-point measurements recorded in the same experiment time. Optimal setting of the two time-points that minimize experimental errors is also discussed. Next we show that the simplistic single time-point measurement that has been commonly used in the literature, can substantially underestimate the true value of Gamma(2), unless a relatively long repetition delay is employed. We then examine the field dependence of Gamma(2), and show that Gamma(2) exhibits only a very weak field dependence at high magnetic fields typically employed in macromolecular studies. The theoretical basis for this observation is discussed. Finally, we investigate the impact of contamination of the paramagnetic sample by trace amounts (5%) of the corresponding diamagnetic species on the accuracy of Gamma(2) measurements. Errors in Gamma(2) introduced by such diamagnetic contamination are potentially sizeable, but can be significantly reduced by using a relatively short time interval for the two time-point Gamma(2) measurement.
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Affiliation(s)
- Junji Iwahara
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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36
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Gooch BD, Krishnamurthy M, Shadid M, Beal PA. Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex. Chembiochem 2006; 6:2247-54. [PMID: 16245373 DOI: 10.1002/cbic.200500285] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Helix-threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptide functionality into the dissimilar duplex grooves. To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. This helix is a component of the binding site for the ribosomal protein S15. In addition, the S15-16S RNA interaction is important for the ordered assembly of the bacterial ribosome. Here we present the synthesis and characterization of helix-threading peptides that bind selectively to helix 22 of E. coli 16S RNA. These compounds bind helix 22 by threading intercalation placing the N termini in the minor groove and the C termini in the major groove. Binding is dependent on the presence of a highly conserved purine-rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl-EDTAFe (MPEFe). Moreover, binding selectivity translates into selective inhibition of formation of the S15-16S complex.
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Affiliation(s)
- Barry D Gooch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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37
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Tang C, Iwahara J, Clore GM. Visualization of transient encounter complexes in protein-protein association. Nature 2006; 444:383-6. [PMID: 17051159 DOI: 10.1038/nature05201] [Citation(s) in RCA: 328] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 09/04/2006] [Indexed: 11/09/2022]
Abstract
Kinetic data on a number of protein-protein associations have provided evidence for the initial formation of a pre-equilibrium encounter complex that subsequently relaxes to the final stereospecific complex. Site-directed mutagenesis and brownian dynamics simulations have suggested that the rate of association can be modulated by perturbations in charge distribution outside the direct interaction surfaces. Furthermore, rate enhancement through non-specific binding may occur by either a reduction in dimensionality or the presence of a short-range, non-specific attractive potential. Here, using paramagnetic relaxation enhancement, we directly demonstrate the existence and visualize the distribution of an ensemble of transient, non-specific encounter complexes under equilibrium conditions for a relatively weak protein-protein complex between the amino-terminal domain of enzyme I and the phosphocarrier protein HPr. Neither the stereospecific complex alone nor any single alternative conformation can account fully for the intermolecular paramagnetic relaxation enhancement data. Restrained rigid-body simulated annealing refinement against the paramagnetic relaxation enhancement data enables us to obtain an atomic probability distribution map of the non-specific encounter complex ensemble that qualitatively correlates with the electrostatic surface potentials on the interacting proteins. Qualitatively similar results are presented for two other protein-protein complexes.
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Affiliation(s)
- Chun Tang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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38
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Zugates GT, Anderson DG, Little SR, Lawhorn IEB, Langer R. Synthesis of Poly(β-amino ester)s with Thiol-Reactive Side Chains for DNA Delivery. J Am Chem Soc 2006; 128:12726-34. [PMID: 17002366 DOI: 10.1021/ja061570n] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The safe and efficient delivery of DNA remains the major barrier to the clinical application of non-viral gene therapy. Here, we present novel, biodegradable polymers for gene delivery that are capable of simple graft modification and demonstrate the ability to respond to intracellular conditions. We synthesized poly(beta-amino ester)s using a new amine monomer, 2-(pyridyldithio)-ethylamine (PDA). These cationic, degradable polymers contain pyridyldithio functionalities in the side chains that react with high specificity toward thiol ligands. This reactivity is demonstrated using both mercaptoethylamine (MEA) and the thiol peptide RGDC, a ligand that binds with high affinity to certain integrin receptors. These two polymer derivatives displayed strong DNA binding as determined using electrophoresis and dye exclusion assays. In addition, the MEA-based polymer and plasmid DNA were shown to self-assemble into cationic complexes with effective diameters as low as 100 nm. Furthermore, this DNA binding ability was substantially reduced in response to intracellular glutathione concentrations, which may aid in DNA unpackaging inside the cell. These complexes also displayed low cellular toxicity and were able to mediate transfection at levels comparable to PEI in human hepatocellular carcinoma cells. These results suggest that PDA-based poly(beta-amino ester)s may serve as a modular platform for polymer-mediated gene delivery.
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Affiliation(s)
- Gregory T Zugates
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building E25-342, Cambridge, MA 02139, USA
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39
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Krishnamurthy M, Gooch BD, Beal PA. RNA binding and thiolytic stability of a quinoline-containing helix-threading peptide. Org Biomol Chem 2006; 4:639-45. [PMID: 16467938 DOI: 10.1039/b513591e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Helix-threading peptides (HTPs) bind selectively to sites predisposed to intercalation in folded RNA molecules placing peptide functional groups into the dissimilar grooves of the duplex. Here we report the design and synthesis of new HTPs with quinoline as the intercalation domain. A quinoline-containing HTP is shown to bind selectively to duplex RNA binding sites. Furthermore, the affinity cleavage pattern generated using an EDTA.Fe modified derivative is consistent with minor groove localization of its N-terminus. This compound binds base-pair steps flanked by single nucleotide bulges on the 3' side on both strands, whereas bulges on the 5' side of the intercalation site do not support binding. Furthermore, unlike acridine HTPs, the quinoline compound is resistant to thiolytic degradation that leads to loss of RNA-binding activity. The RNA-binding selectivity and stability observed for quinoline-containing HTPs make them excellent candidates for further development as regulators of intracellular RNA function.
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Affiliation(s)
- Malathy Krishnamurthy
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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40
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Nakatsukasa T, Shiraishi Y, Negi S, Imanishi M, Futaki S, Sugiura Y. Site-specific DNA cleavage by artificial zinc finger-type nuclease with cerium-binding peptide. Biochem Biophys Res Commun 2005; 330:247-52. [PMID: 15781257 DOI: 10.1016/j.bbrc.2005.02.164] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Indexed: 11/18/2022]
Abstract
The addition of a new function to native proteins is one of the most attractive protein-based designs. In this study, we have converted a C(2)H(2)-type zinc finger as a DNA-binding motif into a novel zinc finger-type nuclease by connecting two distinct zinc finger proteins (Sp1 and GLI) with a functional linker possessing DNA cleavage activity. As a DNA cleavage domain, we chose an analogue of the metal-binding loop (12 amino acid residues), peptide P1, which has been reported to exhibit a strong binding affinity for a lanthanide ion and DNA cleavage ability in the presence of Ce(IV). Our newly designed nucleases, Sp1(P1)GLI and Sp1(P1G)GLI, can strongly bind to a lanthanide ion and show a unique DNA cleavage pattern, in which certain positions between the two DNA-binding sites are specifically cleaved. The present result provides useful information for expanding the design strategy for artificial nucleases.
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Affiliation(s)
- Takako Nakatsukasa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Abstract
Many important biological processes, from the interferon antiviral response to the generation of microRNA regulators of translation, involve duplex RNA. Small molecules capable of binding duplex RNA structures with high affinity and selectivity will be useful in regulating these processes and, as such, are valuable research tools and potentially therapeutic. In this paper, the synthesis and duplex RNA-binding properties of EDTA.Fe-modified peptide-intercalator conjugates (PICs) are described. Peptide appendages at the 4- and 9-positions of the planar acridine ring system render these PICs threading intercalators, directing the substituents into both grooves of double helical RNA simultaneously. Directed hydroxyl radical cleavage experiments conducted with varying RNA stem-loop structures indicate a preferred binding polarity with the N- and C-termini of the PIC in the minor and major grooves, respectively. However, this binding polarity is shown to be dependent on both the structure of the PIC and the RNA secondary structure adjacent to the intercalation site. Definition of the minimal RNA structure required for binding to one of these PICs led to the identification of an intercalation site in a pre-microRNA from Caenorhabditis elegans. Results presented will guide both rational design and combinatorial approaches for the generation of new RNA binding PICs and will continue to facilitate the identification of naturally occurring RNA targets for these small molecules.
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Affiliation(s)
- Barry D Gooch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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42
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Bruno M, Flaus A, Owen-Hughes T. Site-specific attachment of reporter compounds to recombinant histones. Methods Enzymol 2004; 375:211-28. [PMID: 14870669 DOI: 10.1016/s0076-6879(03)75014-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Affiliation(s)
- Michael Bruno
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, Department of Biochemistry, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
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Flaus A, Owen-Hughes T. Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Mol Cell Biol 2003; 23:7767-79. [PMID: 14560021 PMCID: PMC207611 DOI: 10.1128/mcb.23.21.7767-7779.2003] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move along DNA via either thermal or enzyme-driven movements. Here we have monitored the movements of nucleosomes following deposition at well-defined locations on mouse mammary tumor virus promoter DNA. We found that the sites to which nucleosomes are deposited during chromatin assembly differ from those favored during thermal equilibration. Taking advantage of this, we were able to track the movement of nucleosomes over 156 bp and found that this proceeds via intermediate positions spaced between 46 and 62 bp. The remodeling enzyme ISWI was found to direct the movement of nucleosomes to sites related to those observed during thermal mobilization. In contrast, nucleosome mobilization driven by the SWI/SNF and RSC complexes were found to drive nucleosomes towards sites up to 51 bp beyond DNA ends, with little respect for the sites favored during thermal repositioning. The dynamic properties of nucleosomes we describe are likely to influence their role in gene regulation.
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Affiliation(s)
- Andrew Flaus
- Division of Gene Regulation and Expression, The Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, United Kingdom
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45
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Guillaumie F, Sterling JD, Jensen KJ, Thomas ORT, Mohnen D. Solid-supported enzymatic synthesis of pectic oligogalacturonides and their analysis by MALDI-TOF mass spectrometry. Carbohydr Res 2003; 338:1951-60. [PMID: 14499571 DOI: 10.1016/s0008-6215(03)00321-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Solid-phase biosynthetic reactions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF), was used to gain insight into the biosynthesis of pectin oligomers. Sepharose supports bearing long pectic oligogalacturonides (OGAs) anchored through a disulfide-containing cleavable linker, were prepared. The OGAs (degrees of polymerization of 13 and 14) were efficiently immobilized through the reducing end via formation of an oxime linkage. These OGA-derivatized matrices were subsequently employed in novel solid-phase enzymatic reactions, with the pectin biosynthetic enzyme, alpha-1,4-galacturonosyltransferase, GalAT (solubilized from Arabidopsis thaliana) and the glycosyl donor, uridine diphosphate-galacturonic acid (UDP-GalA). Solid-supported biosynthesis was followed by cleavage of the immobilized OGAs and direct analysis of the products released into the liquid phases by MALDI-TOF mass spectrometry. In time course studies conducted with an immobilized (alpha-D-GalA)14 and limiting amounts of the glycosyl donor, the predominant product was an OGA extended by one GalA residue at the non-reducing end (i.e., (GalA)15). When UDP-GalA was added in approximately excess compared to immobilized (GalA)13, OGAs up to the 16-mer were synthesized, confirming the non-processivity of the GalAT in vitro.
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Affiliation(s)
- Fanny Guillaumie
- Center for Process Biotechnology, BioCentrum-DTU, Technical University of Denmark, Building 223, Søltofts Plads, DK-2800 Kgs Lyngby, Denmark
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46
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Carlson CB, Vuyisich M, Gooch BD, Beal PA. Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution. CHEMISTRY & BIOLOGY 2003; 10:663-72. [PMID: 12890540 DOI: 10.1016/s1074-5521(03)00147-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5'-CpG-3' sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (K(D) = 20 nM) contains a base-paired 5'-CpG-3' step flanked on the 5' side by a 4 nt internal loop and the 3' side by a bulged U. Several viral 5'- and 3'-UTR RNA sequences that likely form binding sites for this PAC are identified.
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Affiliation(s)
- Coby B Carlson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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47
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Bell SA, McLean ME, Oh SK, Tichy SE, Zhang W, Corn RM, Crooks RM, Simanek EE. Synthesis and characterization of covalently linked single-stranded DNA oligonucleotide-dendron conjugates. Bioconjug Chem 2003; 14:488-93. [PMID: 12643761 DOI: 10.1021/bc020075n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A solution-phase synthesis and characterization of covalent DNA-dendron conjugates is presented. Thiol-terminated 12-base oligonucleotides were added to second- and third-generation triazine-based dendrons via thiol/disulfide exchange chemistry. Single-stranded DNA oligonucleotides were successfully attached to dendrons at the core, the periphery, and both. Proof of structure for these architectures is derived primarily from mass spectrometry and polyacrylamide gel electrophoresis and complemented by labeling analysis using Ellman's reagent and degradation analysis using a reducing agent.
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Affiliation(s)
- Stephen A Bell
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station 77842-3012, USA
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48
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Meares CF, Datwyler SA, Schmidt BD, Owens J, Ishihama A. Principles and methods of affinity cleavage in studying transcription. Methods Enzymol 2003; 371:82-106. [PMID: 14712693 DOI: 10.1016/s0076-6879(03)71006-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Claude F Meares
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616-5295, USA
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49
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Dvoretsky A, Gaponenko V, Rosevear PR. Derivation of structural restraints using a thiol-reactive chelator. FEBS Lett 2002; 528:189-92. [PMID: 12297302 DOI: 10.1016/s0014-5793(02)03297-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recognition and identification of protein folds is a prerequisite for high-throughput structural genomics. Here we demonstrate a simple protocol for covalent attachment of a short and more rigid metal-chelating tag, thiol-reactive EDTA, by chemical modification of the single cysteine residue in barnase(H102C). Conjugation of the metal-chelating tag provides the advantage of allowing a greater range of paramagnetic metal substitutions. Substitution of Yb(3+), Mn(2+), and Co(2+) permitted measurement of metal-amide proton distances, dipolar shifts, and residual dipolar couplings. Paramagnetic-derived restraints are advantageous in the NMR structure elucidation of large protein complexes and are shown sufficient for validation of homology-based fold predictions.
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Affiliation(s)
- Alex Dvoretsky
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, OH 45267, USA
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50
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Guillaumie F, Thomas ORT, Jensen KJ. Immobilization of pectin fragments on solid supports: novel coupling by thiazolidine formation. Bioconjug Chem 2002; 13:285-94. [PMID: 11906266 DOI: 10.1021/bc0155364] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As a prerequisite to solid-phase and sequence analyses and for the study of the fine structure of pectin, we have developed oriented and chemoselective methodologies to couple model pectin fragments onto a solid support. Polyethylene glycol polyacrylamide (PEGA) resins were selected due to their excellent swelling properties in a wide range of solvents, including water, and their easy accessibility to enzymes. Following appropriate derivatization of amino-terminated PEGA resins, oligomers of alpha-D-galacturonic acid (GalA), up to the trimer, were anchored to the support through their reducing end. In addition to reductive amination, the strategies included the formation of an oxime bond, a glycosyl hydrazide, and a pyroglutamyl ring. Further, we developed a new immobilization approach based on the formation of a thiazolidine ring. All methods proved efficient and did not require modification of the GalA oligomers prior to coupling. In addition, very mild conditions and few steps for derivatization of the support were required. Immobilization by thiazolidine ring and oxime bond formation were the preferred methods, given the stability of the linkages formed, their compatibility with aqueous solvents, the few number of steps required, and their potential for application to larger pectin fragments. Thiazolidine and pyroglutamyl anchoring were developed further by the insertion of a disulfide bond which allowed release of the saccharides under mild, selective conditions.
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Affiliation(s)
- Fanny Guillaumie
- Department of Chemistry, Building 201, Kemitorvet, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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