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Nagaraj K, Priyanshi J, Govindasamy C, Sivakumar AS, Kamalesu S, Naman J, Dixitkumar M, Lokhandwala S, Parekh NM, Radha S, Uthra C, Vaishnavi E, Sakthinathan S, Chiu TW, Karuppiah C. Effect of hydrophobicity and size of the ligands on the intercalative binding interactions of some metallo-surfactants containing π-conjugated systems with yeast tRNA. J Biomol Struct Dyn 2024; 42:3949-3957. [PMID: 37254288 DOI: 10.1080/07391102.2023.2216783] [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] [Received: 02/12/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023]
Abstract
The intercalative yeast t-RNA binding behavior of some metallo-surfactant complexes, Co(ip)2(TA)2](ClO4)3 (1) and [Co(dpq)2(TA)2](ClO4)3 (2) where TA = Tetradecylamine (Myristylamine), ip = imidazo[4,5-f][1,10]phenanthroline and dpq = dipyrido[3,2-d:2'-3'-f]quinoxaline containing π-conjugated systems (both below and above critical micelle concentration) have been investigated by means of absorption spectral titration, competitive binding, circular dichroism, cyclic voltammetry, and viscometry measurements. Absorption spectral titration results implicate yeast tRNA has significant effects on the binding behaviors of two surfactant complexes via intercalative mode showed a significant absorption band of hypochromicity with red shift. The intrinsic binding constant values below and above CMC were determined as Kb = 6.12 × 105 M-1, 2.31 × 106 M-1, for complex (1) and 7.23 × 105 M-1, 3.57 × 106 M-1, for complex (2). In both sets of complexes (1) and (2), the complexes bind more strongly to yeast tRNA in the above critical micelle concentration can be hydrophobic and confirm intercalation. Competitive displacement studies confirmed that complexes bind to yeast tRNA via intercalative mode. Cyclic voltammetry studies suggest the increasing amounts of yeast tRNA, the cathodic potential Epc for the two complexes shows a positive shift in peak potential indicated the process of binding via intercalation. These observations were further validated by CD, and hydrodynamic measurements. All these studies suggesting that a surfactant complex binds to yeast tRNA appear to be mainly intercalative because of hydrophobicity due to extending aromaticity of the π system of the ligand and planarity of the complex has a significant effect on tRNA binding affinity increasing in the order of complexes containing ligands ip < dpq.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karuppiah Nagaraj
- SRICT-Institute of Science and Research, Department of Chemistry, UPL University of Sustainable Technology, Vataria, India
| | - Jigeshkumar Priyanshi
- SRICT-Institute of Science and Research, Department of Chemistry, UPL University of Sustainable Technology, Vataria, India
| | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Allur Subramaniyan Sivakumar
- Department of Orthopaedic Surgery, Dongtan Sacred Heart Hospital, Hallym University, College of Medicine, Hwaseong, Republic of Korea
| | - Supramanium Kamalesu
- Department of Chemistry, University of Science, Chandigarh University, Gharuan, India
| | - Jitendrabhai Naman
- SRICT-Institute of Science and Research, Department of Chemistry, UPL University of Sustainable Technology, Vataria, India
| | - Manojkumar Dixitkumar
- SRICT-Institute of Science and Research, Department of Chemistry, UPL University of Sustainable Technology, Vataria, India
| | - Snehal Lokhandwala
- Department of Environmental Science & Technology, UPL University of Sustainable Technology, Vataria, India
| | - Nikhil M Parekh
- SRICT-Institute of Science and Research, Department of Chemistry, UPL University of Sustainable Technology, Vataria, India
| | - Suriyan Radha
- Department of Chemistry, Saiva Bhanu Kshatriya College, Aruppukkottai, India
| | - Chandrabose Uthra
- Department of Microbiology, Bharathidasan University, Tiruchirapalli, India
| | - Ellappan Vaishnavi
- Department of Chemistry, Sri GVG Visalakshi College for Women, Udumalpet, India
| | - Subramanian Sakthinathan
- Department of Materials and Mineral Resources Engineering, National Taipei University of Technology, Taipei, Taiwan, ROC
| | - Te-Wei Chiu
- Department of Materials and Mineral Resources Engineering, National Taipei University of Technology, Taipei, Taiwan, ROC
| | - Chelladurai Karuppiah
- Battery Research Center for Green Energy, Ming Chi University of Technology, New Taipei City, Taiwan, ROC
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2
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Theoretical studies on the electronic and optoelectronic properties of DNA/RNA hybrid-metal complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.115015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Patra D, Banerjee S, Sova Mandi C, Haseena KS, Basu G, Dutta S. A Pyrimido-Quinoxaline Fused Heterocycle Lights Up Transfer RNA upon Binding at the Mg 2+ Binding Site. Chembiochem 2020; 22:359-363. [PMID: 32869357 DOI: 10.1002/cbic.202000584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 11/07/2022]
Abstract
Transfer RNAs (tRNAs) are fundamental molecules in cellular translation. In this study we have highlighted a fluorescence-based perceptive approach for tRNAs by using a quinoxaline small molecule. We have synthesised a water-soluble fluorescent pyrimido-quinoxaline-fused heterocycle containing a mandatory piperazine tail (DS1) with a large Stokes shift (∼160 nm). The interaction between DS1 and tRNA results in significant fluorescence enhancement of the molecule with Kd ∼5 μM and multiple binding sites. Our work reveals that the DS1 binding site overlaps with the specific Mg2+ ion binding site in the D loop of tRNA. As a proof-of-concept, the molecule inhibited Pb2+ -induced cleavage of yeast tRNAPhe in the D loop. In competitive binding assays, the fluorescence of DS1-tRNA complex is quenched by a known tRNA-binder, tobramycin. This indicates the displacement of DS1 and, indeed, a substantiation of specific binding at the site of tertiary interaction in the central region of tRNA. The ability of compound DS1 to bind tRNA with a higher affinity compared to DNA and single-stranded RNA offers a promising approach to developing tRNA-based biomarker diagnostics in the future.
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Affiliation(s)
- Dipendu Patra
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India.,Academy of Scientific and Innovative Research (AcSIR) CSIR - Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Sayanika Banerjee
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Chandra Sova Mandi
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - K S Haseena
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India.,Academy of Scientific and Innovative Research (AcSIR) CSIR - Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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Botti V, Urbanelli L, Sagini K, Tarpani L, Cesaretti A, Fortuna CG, Elisei F. Quaternized styryl-azinium fluorophores as cellular RNA-binders. Photochem Photobiol Sci 2020; 19:362-370. [PMID: 32147676 DOI: 10.1039/c9pp00465c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The capability of three quaternized styryl-azinium iodides to bind cellular RNA has been tested by means of Fluorescence Confocal Microscopy imaging of stained MCF-7 cells treated with RNase. Their association constants have been estimated through spectrophotometric and fluorimetric titrations with tRNA and compared to their affinity toward DNA. Transient absorption spectroscopy with femtosecond resolution confirmed the binding of the investigated compounds with tRNA and shed new light on the excited state dynamics of their complexes, by revealing a significant lengthening of the lifetime of S1 upon complexation, which parallels the fluorescence quantum yield enhancement.
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Affiliation(s)
- Valentina Botti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.
| | - Lorena Urbanelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, 06126, Perugia, Italy
| | - Krizia Sagini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, 06126, Perugia, Italy
| | - Luigi Tarpani
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Cosimo G Fortuna
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125, Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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7
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Shin Y, Choi BS, Kim KC, Kang C, Kim K, Yoon CH. Development of a dual reporter screening assay for distinguishing the inhibition of HIV Tat-mediated transcription from off-target effects. J Virol Methods 2017; 249:1-9. [PMID: 28807730 DOI: 10.1016/j.jviromet.2017.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/29/2022]
Abstract
Human immunodeficiency virus (HIV) encodes a transcription trans-activator (Tat) with an essential role in the transcriptional elongation of viral RNA based on the viral promoter long terminal repeat (LTR). Tat-mediated transcription is conserved and can be distinguished from host transcription, so it is a therapeutic target for combating HIV replication. Traditional screening assays for Tat-mediated transcriptional inhibitors are based on the biochemical properties of Tat and transactivation-responsive RNA. We developed an inducible system based on two lentiviral expression cassettes for doxycycline (Dox)-inducible Tat and Renilla luciferase (R-Luc) using TZM-bl cells harboring LTR-driven firefly luciferase (F-Luc). The cells simultaneously expressed both Tat-induced F-Luc and R-Luc, so it was possible to recognize off-target effects in the presence of Dox. The system was validated with known inhibitors: CYC202 obtained high sensitivity and specificity, whereas 6Bio and DRB had off-target effects. The MTT-based cytotoxicity test indicated the resistance of the system even at concentrations with off-target effects. The specificity of the system was confirmed using antiretroviral drugs. Our dual reporter system can simply detect Tat inhibitory effects, as well as precisely discriminate between the inhibitory and off-target effects of inhibitors, and may be useful for the development of a therapeutic anti-HIV drug.
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Affiliation(s)
- YoungHyun Shin
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Byeong-Sun Choi
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Kyung-Chang Kim
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Chun Kang
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Diseases, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Kisoon Kim
- Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Cheol-Hee Yoon
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
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8
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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9
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Sommer G, Fedarovich A, Kota V, Rodriguez R, Smith CD, Heise T. Applying a high-throughput fluorescence polarization assay for the discovery of chemical probes blocking La:RNA interactions in vitro and in cells. PLoS One 2017; 12:e0173246. [PMID: 28291789 PMCID: PMC5349447 DOI: 10.1371/journal.pone.0173246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/18/2017] [Indexed: 12/14/2022] Open
Abstract
The RNA-binding protein La is overexpressed in a number of tumor tissues and is thought to support tumorigenesis by binding to and facilitating the expression of mRNAs encoding tumor-promoting and anti-apoptotic factors. Hence, small molecules able to block the binding of La to specific RNAs could have a therapeutic impact by reducing the expression of tumor-promoting and anti-apoptotic factors. Toward this novel therapeutic strategy, we aimed to develop a high-throughput fluorescence polarization assay to screen small compound libraries for molecules blocking the binding of La to an RNA element derived from cyclin D1 mRNA. Herein, we make use of a robust fluorescence polarization assay and the validation of primary hits by electrophoretic mobility shift assays. We showed recently that La protects cells against cisplatin treatment by stimulating the protein synthesis of the anti-apoptotic factor Bcl2. Here, we show by RNA immunoprecipitation experiments that one small compound specifically impairs the association of La with Bcl2 mRNA in cells and sensitizes cells for cipslatin-induced cell death. In summary, we report the application of a high-throughput fluorescence polarization assay to identify small compounds that impair the binding of La to target RNAs in vitro and in cells.
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Affiliation(s)
- Gunhild Sommer
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Alena Fedarovich
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Venkatesh Kota
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Reycel Rodriguez
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Charles D. Smith
- Department of Pharmaceutical and Biomedical Sciences, 173 Ashley Avenue, Charleston, SC, United States of America
| | - Tilman Heise
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, 173 Ashley Avenue, Charleston, SC, United States of America
- * E-mail:
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10
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Agarwal S, Tyagi G, Chadha D, Mehrotra R. Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 166:1-11. [PMID: 27838504 DOI: 10.1016/j.jphotobiol.2016.09.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 09/18/2016] [Accepted: 09/20/2016] [Indexed: 11/19/2022]
Abstract
Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (Ka) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×102M-1, 4.923×102M-1 and 4.223×102M-1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and efficient RNA targeted chemotherapeutic agents.
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Affiliation(s)
- Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Gunjan Tyagi
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Deepti Chadha
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India.
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11
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Abstract
In this issue of Cancer Cell, Gu et al. characterize small molecules that inhibit the interaction of Mdm2 with the mRNA that encodes the anti-apoptotic XIAP, simultaneously decreasing expression of both proteins. This represents a novel approach that has relevance in tumor cells independent of p53 status.
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Affiliation(s)
- Stephen Bohlman
- Department of Oncological Sciences and The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Manfredi
- Department of Oncological Sciences and The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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12
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Ray B, Agarwal S, Kadian H, Gambhir K, Sharma P, Mehrotra R. Deciphering molecular aspects of interaction between anticancer drug mitoxantrone and tRNA. J Biomol Struct Dyn 2016; 35:2090-2102. [DOI: 10.1080/07391102.2016.1213185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Heena Kadian
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Kaweri Gambhir
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Parag Sharma
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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13
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Abstract
Telomerase activity is responsible for the maintenance of chromosome end structures (telomeres) and cancer cell immortality in most human malignancies, making telomerase an attractive therapeutic target. The rationale for targeting components of the telomerase holoenzyme has been strengthened by accumulating evidence indicating that these molecules have extra-telomeric functions in tumour cell survival and proliferation. This Review discusses current knowledge of the biogenesis, structure and multiple functions of telomerase-associated molecules intertwined with recent advances in drug discovery approaches. We also describe the fertile ground available for the pursuit of next-generation small-molecule inhibitors of telomerase.
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Affiliation(s)
- Greg M Arndt
- Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Karen L MacKenzie
- Personalised Medicine Program, Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
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rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines. Antimicrob Agents Chemother 2016; 60:4433-41. [PMID: 27246781 DOI: 10.1128/aac.00594-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tetracycline antibiotics are known to be effective in the treatment of both infectious and noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the antibacterial action of the tetracyclines does not explain their activity against viruses, protozoa that lack mitochondria, and noninfectious conditions. Also, the mechanism by which the tetracyclines selectively inhibit microbial protein synthesis against host eukaryotic protein synthesis despite conservation of ribosome structure and functions is still questionable. Many studies have investigated the binding of the tetracyclines to the 16S rRNA using the small ribosomal subunit of different bacterial species, but there seems to be no agreement between various reports on the exact binding site on the 16S rRNA. The wide range of activity of the tetracyclines against a broad spectrum of bacterial pathogens, viruses, protozoa, and helminths, as well as noninfectious conditions, indicates a more generalized effect on RNA. In the light of recent evidence that the tetracyclines bind to various synthetic double-stranded RNAs (dsRNAs) of random base sequences, suggesting that the double-stranded structures may play a more important role in the binding of the tetracyclines to RNA than the specific base pairs, as earlier speculated, it is imperative to consider possible alternative binding modes or sites that could help explain the mechanisms of action of the tetracyclines against various pathogens and disease conditions.
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Sinoy S, Fayaz SM, Charles KD, Suvanish VK, Kapfhammer JP, Rajanikant GK. Amikacin Inhibits miR-497 Maturation and Exerts Post-ischemic Neuroprotection. Mol Neurobiol 2016; 54:3683-3694. [DOI: 10.1007/s12035-016-9940-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 05/11/2016] [Indexed: 10/25/2022]
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16
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Interaction of the tetracyclines with double-stranded RNAs of random base sequence: new perspectives on the target and mechanism of action. J Antibiot (Tokyo) 2016; 69:622-30. [PMID: 26786504 DOI: 10.1038/ja.2015.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/02/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023]
Abstract
The 16S rRNA binding mechanism proposed for the antibacterial action of the tetracyclines does not explain their mechanism of action against non-bacterial pathogens. In addition, several contradictory base pairs have been proposed as their binding sites on the 16S rRNA. This study investigated the binding of minocycline and doxycycline to short double-stranded RNAs (dsRNAs) of random base sequences. These tetracyclines caused a dose-dependent decrease in the fluorescence intensities of 6-carboxyfluorescein (FAM)-labelled dsRNA and ethidium bromide (EtBr)-stained dsRNA, indicating that both drugs bind to dsRNA of random base sequence in a manner that is competitive with the binding of EtBr and other nucleic acid ligands often used as stains. This effect was observable in the presence of Mg(2+). The binding of the tetracyclines to dsRNA changed features of the fluorescence emission spectra of the drugs and the CD spectra of the RNA, and inhibited RNase III cleavage of the dsRNA. These results indicate that the double-stranded structures of RNAs may have a more important role in their interaction with the tetracyclines than the specific base pairs, which had hitherto been the subject of much investigation. Given the diverse functions of cellular RNAs, the binding of the tetracyclines to their double-stranded helixes may alter the normal processing and functioning of the various biological processes they regulate. This could help to explain the wide range of action of the tetracyclines against various pathogens and disease conditions.
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Tyagi G, Agarwal S, Mehrotra R. tRNA binding with anti-cancer alkaloids–nature of interaction and comparison with DNA–alkaloids adducts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 142:250-6. [DOI: 10.1016/j.jphotobiol.2014.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/01/2014] [Accepted: 12/06/2014] [Indexed: 11/26/2022]
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Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S. Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Res 2013; 41:3819-32. [PMID: 23393189 PMCID: PMC3616728 DOI: 10.1093/nar/gkt063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 01/17/2023] Open
Abstract
The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A-U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch.
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MESH Headings
- Alternative Splicing/drug effects
- Base Sequence
- Exons
- HEK293 Cells
- High-Throughput Screening Assays
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Pyrvinium Compounds/metabolism
- Pyrvinium Compounds/pharmacology
- RNA Editing
- RNA Precursors/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Messenger/metabolism
- Receptor, Serotonin, 5-HT2C/genetics
- Receptor, Serotonin, 5-HT2C/metabolism
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stanislav Bellaousov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Michael Hiller
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Pierre de La Grange
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Trevor P. Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Orit Malina
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Ruth Sperling
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - David H. Mathews
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Peter Stoilov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
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Basu A, Jaisankar P, Suresh Kumar G. Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.). PLoS One 2013; 8:e58279. [PMID: 23526972 PMCID: PMC3602459 DOI: 10.1371/journal.pone.0058279] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/01/2013] [Indexed: 12/19/2022] Open
Abstract
Background Three new analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore along with berberrubine were studied for their binding to tRNAphe by wide variety of biophysical techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry. Methodology/Principal Findings Scatchard binding isotherms revealed that the cooperative binding mode of berberine was propagated in the analogs also. Thermal melting studies showed that all the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs stabilized the tRNAphe more in comparison to berberine. Circular dichroism studies showed that these analogs perturbed the structure of tRNAphe more in comparison to berberine. Ferrocyanide quenching studies and viscosity results proved the intercalative binding mode of these analogs into the helical organization of tRNAphe. The binding was entropy driven for the analogs in sharp contrast to the enthalpy driven binding of berberine. The introduction of the aryl/arylalkyl amino carbonyl methyl substituent at the 9-position thus switched the enthalpy driven binding of berberine to entropy dominated binding. Salt and temperature dependent calorimetric studies established the involvement of multiple weak noncovalent interactions in the binding process. Conclusions/Significance The results showed that 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs exhibited almost ten folds higher binding affinity to tRNAphe compared to berberine whereas the binding of berberrubine was dramatically reduced by about twenty fold in comparison to berberine. The spacer length of the substitution at the 9-position of the isoquinoline chromophore appears to be critical in modulating the binding affinities towards tRNAphe.
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Affiliation(s)
- Anirban Basu
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Gopinatha Suresh Kumar
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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20
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Strategies to Block HIV Transcription: Focus on Small Molecule Tat Inhibitors. BIOLOGY 2012; 1:668-97. [PMID: 24832514 PMCID: PMC4009808 DOI: 10.3390/biology1030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023]
Abstract
After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription.
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21
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Miller BL. DCC in the development of nucleic acid targeted and nucleic acid inspired structures. Top Curr Chem (Cham) 2012; 322:107-37. [PMID: 21769715 DOI: 10.1007/128_2011_200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Nucleic acids were one of the first biological targets explored with DCC, and research into the application has continued to yield novel and useful structures for sequence- and structure-selective recognition of oligonucleotides. This chapter reviews major developments in DNA- and RNA-targeted DCC, including methods under development for the conversion of DCC-derived lead compounds into probe molecules suitable for studies in vitro and in vivo. Innovative applications of DCC for the discovery of new materials based on nucleic acids and new methods for the modification of nucleic acid structure and function are also discussed.
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Affiliation(s)
- Benjamin L Miller
- Department of Dermatology, University of Rochester Medical Center, Rochester, NY 14642, USA.
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22
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Zhang J, Umemoto S, Nakatani K. Fluorescent Indicator Displacement Assay for Ligand−RNA Interactions. J Am Chem Soc 2010; 132:3660-1. [DOI: 10.1021/ja100089u] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinhua Zhang
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
| | - Shiori Umemoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
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23
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Holcomb DR, Ropp PA, Theil EC, Thorp HH. Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex. Inorg Chem 2010; 49:786-95. [PMID: 20038124 PMCID: PMC2812480 DOI: 10.1021/ic9008619] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Oxidation of RNA can be effected by two different techniques: a photochemical, electron-transfer method termed "flash-quench" and direct oxidation by metal oxo complexes. The flash-quench method produces selective oxidation using a metal photosensitizer, tris(bipyridyl)ruthenium(III) trichloride (Ru(bpy)(3)(3+)), and quencher, pentaamminechlorocobalt(III) chloride (Co(NH(3))(5)Cl(2+)). We have optimized the flash-quench technique for the following RNAs: tRNA(Phe), human ferritin iron-responsive element (IRE), and a mutated human ferritin IRE. We have also employed a chemical footprinting technique involving the oxoruthenium(IV) complex (Ru(tpy)(bpy)O(2+) (tpy = 2,2',2''-terpyridine; bpy = 2,2'-bipyridine)) to oxidize guanine. Comparison of the two methods shows that the flash-quench technique provides a visualization of nucleotide accessibility for a static conformation of RNA while the Ru(tpy)(bpy)O(2+) complex selectively oxidizes labile guanines and gives a visualization of a composite of multiple conformations of the RNA structure.
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Affiliation(s)
- Dana R. Holcomb
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Patricia A. Ropp
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Elizabeth C. Theil
- Center for BioIron at the Children’s Hospital of Oakland Research Institute, Oakland, CA 94609
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720-3104
| | - H. Holden Thorp
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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Baugh C, Wang S, Li B, Appleman JR, Thompson PA. SCAN--a high-throughput assay for detecting small molecule binding to RNA targets. ACTA ACUST UNITED AC 2009; 14:219-29. [PMID: 19211778 DOI: 10.1177/1087057108330111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel optical-based high-throughput screening technology has been developed for increasing the rate of discovering chemical leads against RNA targets. SCAN ( Screen for Compounds with Affinity for Nucleic Acids) is an affinity-based assay that identifies small molecules that bind and recognize structured RNA elements. This technology provides the opportunity to conduct high-throughput screening of a new class of targets-RNA. SCAN offers many attractive features including a simple homogeneous format, low screening costs, and the ability to use common laboratory equipment. A SCAN assay was developed for the HCV IRES Loop IIId RNA domain. A high-throughput screen of our entire compound library resulted in the identification of small molecule ligands that bind to Loop IIId. The Z' values were greater than 0.8, showing this to be a robust high-throughput screening assay. A correlation between SCAN EC50 and KD values is reported suggesting the ability to use the assay for compound optimization.
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Affiliation(s)
- Chris Baugh
- Department of Biology, Anadys Pharmaceuticals, Inc., San Diego, California 92121, USA
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26
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Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Canzoneri JC, Oyelere AK. Interaction of anthracyclines with iron responsive element mRNAs. Nucleic Acids Res 2008; 36:6825-34. [PMID: 18953029 PMCID: PMC2588532 DOI: 10.1093/nar/gkn774] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Double-stranded sections of mRNA are often inviting sites of interaction for a wide variety of proteins and small molecules. Interactions at these sites can serve to regulate, or disrupt, the homeostasis of the encoded protein products. Such ligand target sites exist as hairpin-loop structures in the mRNAs of several of the proteins involved in iron homeostasis, including ferritin heavy and light chains, and are known as iron responsive elements (IREs). These IREs serve as the main control mechanism for iron metabolism in the cell via their interaction with the iron regulatory proteins (IRPs). Disruption of the IRE/IRP interaction could greatly affect iron metabolism. Here, we report that anthracyclines, a class of clinically useful chemotherapeutic drugs that includes doxorubicin and daunorubicin, specifically interact with the IREs of ferritin heavy and light chains. We characterized this interaction through UV melting, fluorescence quenching and drug-RNA footprinting. Results from footprinting experiments with wild-type and mutant IREs indicate that anthracyclines preferentially bind within the UG wobble pairs flanking an asymmetrically bulged C-residue, a conserved base that is essential for IRE-IRP interaction. Additionally, drug-RNA affinities (apparent K(d)s) in the high nanomolar range were calculated from fluorescence quenching experiments, while UV melting studies revealed shifts in melting temperature (DeltaT(m)) as large as 10 degrees C. This anthracycline-IRE interaction may contribute to the aberration of intracellular iron homeostasis that results from anthracycline exposure.
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Affiliation(s)
- Joshua C Canzoneri
- School of Chemistry and Biochemistry, Parker H Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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28
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Kumar R, Garneau P, Nguyen N, William Lown J, Pelletier J. Methionine Sustituted Polyamides are RNAse Mimics that Inhibit Translation. J Drug Target 2008; 12:125-34. [PMID: 15203891 DOI: 10.1080/1061186042000220728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
RNAse mimics are small molecules that can cleave RNA in a fashion similar to ribonucleases. These compounds would be very useful as gene specific reagents if their activities could be regulated and targeted. We demonstrate here that polyamides with methionine substituents show enhanced RNA cleavage activity relative to other polyamides. Conjugation of these compounds to aminoglycosides produced RNAse mimics that are capable of inhibiting eukaryotic protein synthesis. As a new class of compounds capable of interacting with nucleic acids, these novel aminoglycoside-polyamides constitute promising scaffolds for the construction of nuclease mimics with biological activity.
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Affiliation(s)
- Rohtash Kumar
- Department of Chemistry University of Alberta Edmonton Alta. Canada
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29
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An RNA microchip containing immobilized oligoribonucleotides with protective groups at 2'-O-positions. Biotechniques 2008; 44:77-83. [PMID: 18254383 DOI: 10.2144/000112677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To analyze RNA interactions with RNA binding molecules an RNA microchip containing immobilized oligoribonucleotides with protective groups [t-butyldimethylsilyl (tBDMS)] at 2'-O- positions was developed. The oligonucleotides were immobilized within three-dimensional (3-D) hydrogel pads fixed on a glass support. The protective groups preserved the oligoribonucleodes from degradation and were suitable to be removed directly on the microchip when needed, right before its use. These immobilized, deprotected oligoribonucleotides were tested for their interaction with afluorescently labeled oligodeoxyribonucleotide and analyzed for their availability to be cleaved enzymatically by the RNase binase. Stability of tBDMS-protected immobilized oligoribonucleotides after 2.5 years of storage as well as after direct RNase action was also tested. Melting curves of short RNA/DNA hybrids that had formed into gel pads of the microchip were found to exhibit clearly defined S-like shapes, with the melting temperatures in full accordance with those theoretically predicted for the same ionic strength. This approach, based on keeping the protective groups attached to oligoribonucleotides, can be applied for manufacturing any RNA microchips containing immobilized oligoribonucleotides, including microchips with two-dimensional (2-D) features. These RNA microchips can be used to measure thermodynamic parameters of RNA/RNA or RNA/DNA duplexes as well as to study ligand- or protein-RNA interactions.
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30
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Abstract
1. RNA interference (RNAi) is a robust method of post-transcriptional silencing of genes using double-stranded RNA (dsRNA) with sequence homology driven specificity. The dsRNA can be between 21 and 23 nucleotides long: this is converted to small interfering RNA (siRNA), which then mediates gene silencing by degradation/blocking of translation of the target mRNA. 2. RNA interference provides a simple, fast and cost-effective alternative to existing gene targeting approaches both in vitro and in vivo. The discovery of siRNAs that cause RNAi in mammalian cells opened the door to the therapeutic use of siRNAs. Highly intense research efforts are now aimed at developing siRNAs for therapeutic purposes. 3. Recent advances in the design and delivery of targeting molecules now allow efficient and highly specific gene silencing in mammalian systems. Synthetic siRNA libraries targeting thousands of mammalian genes are publicly available for high-throughput genetic screens for target discovery and validation. Recent studies have demonstrated the clinical potential of aptly designed siRNAs in various types of viral infections, cancer and renal and neurodegenerative disorders. 4. The present review provides insight into the novel therapeutic strategies of siRNA technology, which is the latest development in nucleic acid-based tools for knocking down gene expression, and its potential for silencing genes associated with various human diseases.
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MESH Headings
- Amyloid Precursor Protein Secretases/genetics
- Amyloid Precursor Protein Secretases/metabolism
- Amyotrophic Lateral Sclerosis/enzymology
- Amyotrophic Lateral Sclerosis/genetics
- Animals
- Clinical Trials as Topic
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Gene Targeting/trends
- Humans
- Huntington Disease/enzymology
- Huntington Disease/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA Interference
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Superoxide Dismutase/genetics
- Superoxide Dismutase/metabolism
- Superoxide Dismutase-1
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Affiliation(s)
- Peter N Pushparaj
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Chao PW, Chow CS. Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching. Bioorg Med Chem 2007; 15:3825-31. [PMID: 17399988 PMCID: PMC2001229 DOI: 10.1016/j.bmc.2007.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 02/27/2007] [Accepted: 03/08/2007] [Indexed: 11/25/2022]
Abstract
Fluorescence of 2-aminopurine (2AP)-substituted A-site and acrylamide quenching were used to study the interactions of paromomycin and neamine with the decoding region of 16S rRNA. The results reveal that paromomycin binding to the A-site RNA leads to increased exposure of residue A1492. In contrast, neamine has little effect on the solvent accessibility of A1492. Electrospray ionization mass spectrometry was used to compare the affinity of paromomycin with the A-site and 2-AP-substituted A-site RNAs.
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Affiliation(s)
- Pei-Wen Chao
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
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32
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Islam MM, Sinha R, Kumar GS. RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium. Biophys Chem 2007; 125:508-20. [PMID: 17156912 DOI: 10.1016/j.bpc.2006.11.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 11/03/2006] [Accepted: 11/03/2006] [Indexed: 11/30/2022]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine with t-RNA(phe) was studied using various biophysical techniques and the data was compared with the binding of the classical DNA intercalator, ethidium. The results of optical thermal melting, differential scanning calorimetry and circular dichroism characterized the native cloverleaf structure of t-RNA under the conditions of the study. The strong binding of the alkaloids and ethidium to t-RNA was revealed from the absorption and fluorescence studies. The salt dependence of the binding constants enabled the dissection of the binding free energy to electrostatic and non-electrostatic contributions. This analysis revealed a surprisingly large favourable component of the non-electrostatic contribution to the binding of these charged alkaloids and ethidium to t-RNA. Isothermal titration calorimetric studies revealed that the binding of both the alkaloids is driven by a moderately favourable enthalpy decrease and a moderately favourable entropy increase while that of ethidium is driven by a large favourable enthalpy decrease. Taken together, the results suggest that the binding of these alkaloid molecules on the t-RNA structure appears to be mostly by partial intercalation while ethidium intercalates to the t-RNA. These results reveal the molecular aspects on the interaction of these alkaloids to t-RNA.
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Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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33
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Sitohy M, Chobert JM, Karwowska U, Gozdzicka-Jozefiak A, Haertlé T. Inhibition of bacteriophage m13 replication with esterified milk proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:3800-6. [PMID: 16719499 DOI: 10.1021/jf0531757] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Esterified milk proteins [methylated (Met) or ethylated (Et) alpha-lactalbumin (ALA), beta-lactoglobulin (BLG), and beta-casein (BCN)], unmodified native milk proteins, and native basic proteins (calf thymus histone and hen egg white lysozyme) were tested for their antiviral activity against the bacteriophage M13 and for their influence on its replication (except BCN). All esterified milk proteins showed an antiviral activity against the bacteriophage M13, proportional to the extent of esterification and, hence, to the increased basicity of the modified proteins. Antiviral activity of 100% Met-BLG disappeared after its pepsinolysis but not after its trypsinolysis. The antiviral activity of Met-BLG was much higher than that of native basic proteins (histone and lysozyme). One hundred percent Met-BLG and 73% Et-BLG inhibited the replication of bacteriophage M13 completely, whereas 60% Met-ALA inhibited phage replication partially. Calf thymus histone inhibited the replication of bacteriophage M13 at a lower extent (20%) than Met- and Et-BLG (100% inhibition). Protein concentration, pH, and concentration of the Escherichia coli culture in the preincubation medium of the virus were other factors influencing antiviral activity. Interactions of esterified proteins with the phage DNA (phenol extracted) followed the same pattern as observed during studies of the inhibition of the phage replication: Met-BLG > Et-BLG > or = Met-ALA.
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Affiliation(s)
- Mahmoud Sitohy
- Institut National de la Recherche Agronomique, Biopolymères, Interactions, Assemblages, Fonctions et Interactions des Protéines Laitières, B.P. 71627, 44316 Nantes Cedex 3, France
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34
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Mao C, Flavin KG, Wang S, Dodson R, Ross J, Shapiro DJ. Analysis of RNA-protein interactions by a microplate-based fluorescence anisotropy assay. Anal Biochem 2006; 350:222-32. [PMID: 16448619 DOI: 10.1016/j.ab.2005.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/29/2005] [Accepted: 12/05/2005] [Indexed: 11/29/2022]
Abstract
Quantitative studies of RNA-protein interactions are quite cumbersome using traditional methods. We developed a rapid microplate-based fluorescence anisotropy (FA)/fluorescence polarization assay that works well, even with RNA probes >90 nucleotides long. We analyzed binding of RNA targets by vigilin/DDP1/SCP160p and by c-myc coding region instability determinant (CRD) binding protein, CRD-BP. Vigilin is essential for cell viability and functions in heterochromatin formation and mRNA decay. The CRD-BP stabilizes c-myc mRNA. Vigilin bound to a vitellogenin mRNA 3'-UTR probe with a two to three-fold lower affinity than to a Drosophila dodecasatellite ssDNA binding site and bound to the c-myc CRD with a two- to three-fold lower affinity than to the vitellogenin mRNA 3'-UTR. Competition between vigilin and CRD-BP for binding to the CRD may therefore play a role in regulating c-myc mRNA degradation. We analyzed suitability of the microplate-based FA assay for high-throughput screening for small-molecule regulators of RNA-protein interactions. The assay exhibits high reproducibility and precision and works well in 384-well plates and in 5 microl to 20 microl samples. To demonstrate the potential of this assay for screening libraries of small molecules to identify novel regulators of RNA-protein interactions, we identified neomycin and H33342 as inhibitors of binding of vigilin to the vitellogenin mRNA 3'-UTR.
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Affiliation(s)
- Chengjian Mao
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801-3602, USA
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35
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Tibodeau JD, Fox PM, Ropp PA, Theil EC, Thorp HH. The up-regulation of ferritin expression using a small-molecule ligand to the native mRNA. Proc Natl Acad Sci U S A 2006; 103:253-7. [PMID: 16381820 PMCID: PMC1326178 DOI: 10.1073/pnas.0509744102] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2005] [Indexed: 01/26/2023] Open
Abstract
The binding of small molecules to distinctive three-dimensional structures in mRNA provides a new dimension in RNA control, previously limited to the targeting of secondary structures with antisense and RNA interference; such targeting can modulate mRNA function and rates of protein biosynthesis. Small molecules that selectively bind the iron-responsive element (IRE), a specific three-dimensional structure in the noncoding region of the ferritin mRNA model that is recognized by the iron-regulatory protein repressor, were identified by using chemical footprinting. The assay used involved an oxoruthenium(IV) complex that oxidizes guanine bases in RNA sequences. Small molecules that blocked oxidation of guanines in the internal loop region were expected to selectively increase the rate of ferritin synthesis, because the internal loop region of the ferritin IRE is distinctive from those of other IREs. The natural product yohimbine was found (based on gel mobility shifts) to block cleavage of the internal loop RNA site by >50% and seemed to inhibit protein binding. In the presence of yohimbine, the rate of biosynthesis of ferritin in a cell-free expression system (rabbit reticulocyte lysate) increased by 40%. Assignment of the IRE-yohimbine interaction as the origin of this effect was supported by a similar increase in synthesis of luciferase protein in a chimera of the IRE and luciferase gene. The identification of a small, drug-like molecule that recognizes a naturally occurring three-dimensional mRNA structure and regulates protein biosynthesis rates raises the possibility that small molecules can regulate protein biosynthesis by selectively binding to mRNA.
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Affiliation(s)
- Jennifer D Tibodeau
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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36
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Novoyatleva T, Tang Y, Rafalska I, Stamm S. Pre-mRNA Missplicing as a Cause of Human Disease. ALTERNATIVE SPLICING AND DISEASE 2006; 44:27-46. [PMID: 17076263 DOI: 10.1007/978-3-540-34449-0_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Regulated alternative splice site selection emerges as one of the most important mechanisms to control the expression of genetic information in humans. It is therefore not surprising that a growing number of diseases are either associated with or caused by changes in alternative splicing. These diseases can be caused by mutation in regulatory sequences of the pre-mRNA or by changes in the concentration of trans-acting factors. The pathological expression of mRNA isoforms can be treated by transferring nucleic acids derivatives into cells that interfere with sequence elements on the pre-mRNA, which results in the desired splice site selection. Recently, a growing number of low molecular weight drugs have been discovered that influence splice site selection in vivo. These findings prove the principle that diseases caused by missplicing events could eventually be cured.
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Affiliation(s)
- Tatyana Novoyatleva
- University of Erlangen, Institute for Biochemistry, Fahrstrasse 17, 91054 Erlangen, Germany
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37
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Krishnamurthy M, Gooch BD, Beal PA. Peptide quinoline conjugates: a new class of RNA-binding molecules. Org Lett 2004; 6:63-6. [PMID: 14703351 DOI: 10.1021/ol036094+] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A synthesis of 4,8-disubstituted 2-phenylquinoline amino acids is reported with the incorporation of one example into a peptide by solid-phase synthesis. The phenylquinoline-containing peptide binds an RNA target with nanomolar affinity (K(D) = 208 nM). The strategy can be used to prepare a variety of 2-substituted quinoline amino acids for alteration of affinity in intercalator peptides. Since quinolones represent an important class of antibacterials, these compounds may be useful in the discovery of new antibacterial agents.
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38
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Detering C, Varani G. Validation of automated docking programs for docking and database screening against RNA drug targets. J Med Chem 2004; 47:4188-201. [PMID: 15293991 DOI: 10.1021/jm030650o] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The increasing awareness of the essential role of RNA in controlling viral replication and in bacterial protein synthesis emphasizes the potential of ribonucleoproteins as targets for developing new antibacterial and antiviral drugs. RNA forms well defined three-dimensional structures with clefts and binding pockets reminiscent of the active sites of proteins. Furthermore, it precedes proteins in the translation pathway; inhibiting the function of a single RNA molecule would result in inhibition of multiple proteins. Thus, small molecules that bind RNA specifically would combine the advantages of antisense and RNAi strategies with the much more favorable medicinal chemistry of small-molecule therapeutics. The discovery of small-molecule inhibitors of RNA with attractive pharmacological potential would be facilitated if we had available effective computational tools of structure-based drug design. Here, we systematically test automated docking tools developed for proteins using existing three-dimensional structures of RNA-small molecule complexes. The results show that the native structures can generally be reproduced to within 2.5 angstroms more than 50-60% of the time. For more than half of the test complexes, the native ligand ranked among the top 10% compounds in a database-scoring test. Through this work, we provide parameters for the validated application of automated docking tools to the discovery of new inhibitors of RNA function.
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Affiliation(s)
- Carsten Detering
- Departments of Chemistry and Biochemistry, University of Washington, Seattle, Washington 98195-1700, USA
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39
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Athanassiou Z, Dias RLA, Moehle K, Dobson N, Varani G, Robinson JA. Structural Mimicry of Retroviral Tat Proteins by Constrained β-Hairpin Peptidomimetics: Ligands with High Affinity and Selectivity for Viral TAR RNA Regulatory Elements. J Am Chem Soc 2004; 126:6906-13. [PMID: 15174860 DOI: 10.1021/ja0497680] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An approach is described to the design of beta-hairpin peptidomimetic ligands for bovine immunodeficiency virus (BIV) Tat protein, which inhibit binding to its transactivator response element (TAR) RNA. A library of peptidomimetics was derived by grafting onto a hairpin-inducing d-Pro-l-Pro template sequences related to the RNA recognition element in Tat. One hairpin mimetic was identified that binds tightly (K(d) approximately 150 nM) to BIV TAR, and another that binds also to HIV-1 TAR RNA (K(d) approximately 1-2 microM). (In the same assay, the wild-type BIV Tat(65-81) peptide binds to BIV TAR with K(d) approximately 50 nM.) The high-affinity BIV-Tat mimetic was shown to adopt a stable beta-hairpin conformation in free solution by NMR methods. Amino acid substitutions in this mimetic were shown to impact on the hairpin structure and to disrupt binding to the RNA. This family of conformationally constrained peptidomimetics affords insights into the structural requirements for binding to TAR RNA and provides a basis for the design of new ligands with increased inhibitory activity and specificity to both BIV and HIV TAR RNAs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Pairing
- Base Sequence
- Cattle
- Electrophoretic Mobility Shift Assay
- Gene Products, tat/chemistry
- Immunodeficiency Virus, Bovine/chemistry
- Immunodeficiency Virus, Bovine/genetics
- Ligands
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Mimicry
- Molecular Sequence Data
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/metabolism
- Protein Structure, Tertiary
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
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Affiliation(s)
- Zafiria Athanassiou
- Organic Chemistry Institute, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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40
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Cavanagh J, Benson LM, Thompson R, Naylor S. In line desalting mass spectrometry for the study of noncovalent biological complexes. Anal Chem 2004; 75:3281-6. [PMID: 14570174 DOI: 10.1021/ac030182q] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrospray ionization-mass spectrometry is becoming widely used as a high-throughput method for the study of biomolecular interactions. It allows for the analysis of complexes from heterogeneous mixtures with high sensitivity and selectivity. In many cases, biomolecules and their complexes must be stored in nonvolatile salt buffers and other solubilizing agents, such as organics or detergents, to maintain stability and integrity. To ensure an efficient electrospray process, desalting and exchanging the biomolecular solutions into a volatile buffer is imperative. Current off-line or on-line methods to accomplish this are time-consuming, frequently disrupt noncovalent interactions, and can result in considerable sample loss. Here we describe a simple, general, and highly efficient, rapid in-line desalting approach using a small gel cartridge to assist in the mass spectrometric analysis of biomolecules and their complexes. Though the method has broad applicability, we focus our analysis on proteins and demonstrate its usefulness by examining protein-metal, protein-protein, protein-DNA, and protein-RNA interactions. The method is shown to provide rapid direct analysis of analyte solutions containing salts, glycerol, organics, and involatile buffers without deleterious effects.
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Affiliation(s)
- John Cavanagh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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41
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Abstract
RNA-proteins interactions are involved in numerous cellular functions. These interactions are found in most cases within complex macromolecular assemblies. The recent development of tools and techniques to study RNA-protein complexes has significantly increased our knowledge in the nature of these specific interactions. The aim of this article is to present the different techniques used to study RNA-protein complexes, as well as recent data concerning the application of RNA as therapeutic molecules.
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Affiliation(s)
- Nicolas Hugo
- Ecole Normale Supérieure de Lyon, Cnrs UMR 5665, 46, allée d'Italie, 69364 Lyon 07, France
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42
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He Y, Yang J, Wu B, Robinson D, Sprankle K, Kung PP, Lowery K, Mohan V, Hofstadler S, Swayze EE, Griffey R. Synthesis and evaluation of novel bacterial rRNA-binding benzimidazoles by mass spectrometry. Bioorg Med Chem Lett 2004; 14:695-9. [PMID: 14741271 DOI: 10.1016/j.bmcl.2003.11.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A series of novel benzimidazoles were efficiently synthesized using both solution- and solid-phase chemistry. These compounds were found to bind to the bacterial 16S ribosomal RNA A-site with micromolar affinities using unique mass spectrometry-based assays.
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Affiliation(s)
- Yun He
- Ibis Therapeutics, A Division of Isis Pharmaceuticals, Inc, 2292 Faraday Av, Carlsbad, CA 92008, USA.
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43
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Affiliation(s)
- Chi-Huey Wong
- Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92307, USA
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44
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Carlson CB, Stephens OM, Beal PA. Recognition of double-stranded RNA by proteins and small molecules. Biopolymers 2003; 70:86-102. [PMID: 12925995 DOI: 10.1002/bip.10413] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular recognition of double-stranded RNA (dsRNA) is a key event for numerous biological pathways including the trafficking, editing, and maturation of cellular RNA, the interferon antiviral response, and RNA interference. Over the past several years, our laboratory has studied proteins and small molecules that bind dsRNA with the goal of understanding and controlling the binding selectivity. In this review, we discuss members of the dsRBM class of proteins that bind dsRNA. The dsRBM is an approximately 70 amino acid sequence motif found in a variety of dsRNA-binding proteins. Recent results have led to a new appreciation of the ability of these proteins to bind selectivity to certain sites on dsRNA. This property is discussed in light of the RNA selectivity observed in the function of two proteins that contain dsRBMs, the RNA-dependent protein kinase (PKR) and an adenosine deaminase that acts on dsRNA (ADAR2). In addition, we introduce peptide-acridine conjugates (PACs), small molecules designed to control dsRBM-RNA interactions. These intercalating molecules bear variable peptide appendages at opposite edges of an acridine heterocycle. This design imparts the potential to exploit differences in groove characteristics and/or base-pair dynamics at binding sites to achieve selective binding.
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Affiliation(s)
- Coby B Carlson
- University of Utah, Department of Chemistry, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA
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45
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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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46
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Chobert JM. Milk protein modification to improve functional and biological properties. ADVANCES IN FOOD AND NUTRITION RESEARCH 2003; 47:1-71. [PMID: 14639781 DOI: 10.1016/s1043-4526(03)47001-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Jean-Marc Chobert
- Laboratoire d'Etude des Interactions des Molécules Alimentaires Institut National de la Recherche Agronomique Rue de la Géraudière B.P. 71627, 44316 Nantés, France
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47
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Stoilov P, Meshorer E, Gencheva M, Glick D, Soreq H, Stamm S. Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol 2002; 21:803-18. [PMID: 12489991 DOI: 10.1089/104454902320908450] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Humans possess a surprisingly low number of genes and intensively use pre-mRNA splicing to achieve the high molecular complexity needed to sustain normal body functions and facilitate responses to altered conditions. Because hundreds of thousands of proteins are generated by 25,000 to 40,000 genes, pre-mRNA processing events are highly important for the regulation of human gene expression. Both inherited and acquired defects in pre-mRNA processing are increasingly recognized as causes of human diseases, and almost all pre-mRNA processing events are controlled by a combination of protein factors. This makes defects in these processes likely candidates for causes of diseases with complicated inheritance patterns that affect seemingly unrelated functions. The elucidation of genetic mechanisms regulating pre-mRNA processing, combined with the development of drugs targeted at consensus RNA sequences and/or corresponding proteins, can lead to novel diagnostic and therapeutic approaches.
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Affiliation(s)
- Peter Stoilov
- University of Erlangen-Nurenberg, Institute of Biochemistry, 91054 Erlangen, Germany
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48
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Abstract
Several rapidly developing RNA interference (RNAi) methodologies hold the promise to selectively inhibit gene expression in mammals. RNAi is an innate cellular process activated when a double-stranded RNA (dsRNA) molecule of greater than 19 duplex nucleotides enters the cell, causing the degradation of not only the invading dsRNA molecule, but also single-stranded (ssRNAs) RNAs of identical sequences, including endogenous mRNAs. As such, RNAi technology is currently being evaluated not only as an extremely powerful instrument for functional genomic analyses, but also as a potentially useful method to develop highly specific dsRNA based gene-silencing therapeutics.
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Affiliation(s)
- David J Shuey
- Nucleonics, 14 Spring Mill Drive, Malvern, PA 19355, USA
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49
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Gambari R. Biospecific interaction analysis: a tool for drug discovery and development. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2002; 1:119-35. [PMID: 12174673 DOI: 10.2165/00129785-200101020-00005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent development of surface plasmon resonance (SPR)-based biosensor technologies for biospecific interaction analysis (BIA) enables the monitoring of a variety of molecular reactions in real-time. The biomolecular interactions occur at the surface of a flow cell of a sensor chip between a ligand immobilized on the surface and an injected analyte. SPR-based BIA offers many advantages over most of the other methodologies available for the study of biomolecular interactions, including full automation, no requirement for labeling, and the availability of a large variety of activated sensor chips that allow immobilization of DNA, RNA, proteins, peptides and cells. The assay is rapid and requires only small quantitities of both ligand and analyte in order to obtain informative results. In addition, the sensor chip can be re-used many times, leading to low running costs. Aside from the analysis of all possible combinations of peptide, protein, DNA and RNA interactions, this technology can also be used for screening of monoclonal antibodies and epitope mapping, analysis of interactions between low molecular weight compounds and proteins or nucleic acids, interactions between cells and ligands, and real-time monitoring of gene expression. Applications of SPR-based BIA in medicine include the molecular diagnosis of viral infections and genetic diseases caused by point mutations. Future perspectives include the combinations of SPR-based BIA with mass spectrometry, the use of biosensors in proteomics, and the application of this technology to design and develop efficient drug delivery systems.
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Affiliation(s)
- R Gambari
- Department of Biochemistry and Molecular Biology, and Biotechnology Center, Ferrara University, Ferrara, Italy.
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50
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Chopra M, Pachuk C, Satishchandran C, Giordano T. Using RNA interference to modulate gene expression. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1477-3627(02)02197-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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