1
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Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
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Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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2
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Wang K, Wang XY, Gao GJ, Ren XW, Cai XY, Yu QK, Xing S, Zhu B. Multistimuli responsive RNA amphiphilic polymeric assembly constructed by calixpyridinium-based supramolecular interactions. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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3
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Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers. Q Rev Biophys 2019; 52:e8. [PMID: 31423956 DOI: 10.1017/s0033583519000064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence turn-on aptamers, in vitro evolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA-fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.
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4
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Rath C, Burger J, Norval L, Kraemer SD, Gensch N, van der Kooi A, Reinemann C, O'Sullivan C, Svobodova M, Roth G. Comparison of different label-free imaging high-throughput biosensing systems for aptamer binding measurements using thrombin aptamers. Anal Biochem 2019; 583:113323. [PMID: 31129134 DOI: 10.1016/j.ab.2019.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 01/18/2023]
Abstract
To enable the analysis of several hundreds to thousands of interactions in parallel, high-throughput systems were developed. We used established thrombin aptamer assays to compare three such high-throughput imaging systems as well as analysis software and user influence. In addition to our own iRIf-system, we applied bscreen and IBIS-MX96. As non-imaging reference systems we used Octet-RED96, Biacore3000, and Monolith-NT.115. In this study we measured 1378 data points. Our results show that all systems are suitable for analyzing binding kinetics, but the kinetic constants as well as the ranking of the selected aptamers depend significantly on the applied system and user. We provide an insight into the signal generation principles, the systems and the results generated for thrombin aptamers. It should contribute to the awareness that binding constants cannot be determined as easily as other constants. Since many parameters like surface chemistry, biosensor type and buffer composition may change binding behavior, the experimenter should be aware that a system and assay dependent KD is determined. Frequently, certain conditions that are best suited for a given biosensing system cannot be transferred to other systems. Therefore, we strongly recommend using at least two different systems in parallel to achieve meaningful results.
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Affiliation(s)
- Christin Rath
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
| | - Juergen Burger
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
| | - Leo Norval
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
| | - Stefan Daniel Kraemer
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany.
| | | | - Christine Reinemann
- Helmholtz Centre for Environmental Research GmbH (UFZ), Permoserstr. 15, 04318, Leipzig, Germany.
| | - Ciara O'Sullivan
- Departament d'Enginyería Química, Universitat Rovira i Virgili, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain.
| | - Marketa Svobodova
- Departament d'Enginyería Química, Universitat Rovira i Virgili, 43007, Tarragona, Spain.
| | - Guenter Roth
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
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5
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Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates. NANOMATERIALS 2018; 8:nano8120984. [PMID: 30486495 PMCID: PMC6315349 DOI: 10.3390/nano8120984] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022]
Abstract
RNA aptamers that bind non-fluorescent dyes and activate their fluorescence are highly sensitive, nonperturbing, and convenient probes in the field of synthetic biology. These RNA molecules, referred to as light-up aptamers, operate as molecular nanoswitches that alter folding and fluorescence function in response to ligand binding, which is important in biosensing and molecular computing. Herein, we demonstrate a conceptually new generation of smart RNA nano-devices based on malachite green (MG)-binding RNA aptamer, which fluorescence output controlled by addition of short DNA oligonucleotides inputs. Four types of RNA switches possessing AND, OR, NAND, and NOR Boolean logic functions were created in modular form, allowing MG dye binding affinity to be changed by altering 3D conformation of the RNA aptamer. It is essential to develop higher-level logic circuits for the production of multi-task nanodevices for data processing, typically requiring combinatorial logic gates. Therefore, we further designed and synthetized higher-level half adder logic circuit by “in parallel” integration of two logic gates XOR and AND within a single RNA nanoparticle. The design utilizes fluorescence emissions from two different RNA aptamers: MG-binding RNA aptamer (AND gate) and Broccoli RNA aptamer that binds DFHBI dye (XOR gate). All computationally designed RNA devices were synthesized and experimentally tested in vitro. The ability to design smart nanodevices based on RNA binding aptamers offers a new route to engineer “label-free” ligand-sensing regulatory circuits, nucleic acid detection systems, and gene control elements.
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6
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A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. Nat Chem Biol 2018; 14:964-971. [PMID: 30061719 PMCID: PMC6143402 DOI: 10.1038/s41589-018-0103-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
Abstract
RNAs directly regulate a vast array of cellular processes, emphasizing the need for robust approaches to fluorescently label and track RNAs in living cells. Here, we develop an RNA imaging platform using the cobalamin riboswitch as an RNA tag and a series of probes containing cobalamin as a fluorescence quencher. This highly modular ‘Riboglow’ platform leverages different colored fluorescent dyes, linkers and riboswitch RNA tags to elicit fluorescent turn-on upon binding RNA. We demonstrate the ability of two different Riboglow probes to track mRNA and small non-coding RNA in live mammalian cells. A side-by-side comparison revealed that Riboglow outperformed the dye binding aptamer Broccoli and performed on par with the gold standard RNA imaging system, the MS2-fluorescent protein system, while featuring a much smaller RNA tag. Together, the versatility of the Riboglow platform and ability to track diverse RNAs suggest broad applicability for a variety of imaging approaches.
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7
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Saha R, Verbanic S, Chen IA. Lipid vesicles chaperone an encapsulated RNA aptamer. Nat Commun 2018; 9:2313. [PMID: 29899431 PMCID: PMC5998061 DOI: 10.1038/s41467-018-04783-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 05/22/2018] [Indexed: 01/08/2023] Open
Abstract
The organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. Here we find that confinement of the malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA. The vesicle effectively ‘chaperones’ the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Encapsulation could thus increase RNA fitness and the likelihood that functional sequences would emerge during the origin of life. So far little is known about how encapsulation affects the activity and folding of RNA, which is of interest for understanding the origin of cellular life. Here the authors show that encapsulation of functional RNA in vesicles increases RNA activity and improves RNA folding through a biophysical confinement effect.
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Affiliation(s)
- Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Samuel Verbanic
- Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA. .,Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, 93106, USA.
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8
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Trachman RJ, Truong L, Ferré-D'Amaré AR. Structural Principles of Fluorescent RNA Aptamers. Trends Pharmacol Sci 2017; 38:928-939. [PMID: 28728963 DOI: 10.1016/j.tips.2017.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/21/2017] [Accepted: 06/21/2017] [Indexed: 11/26/2022]
Abstract
Several aptamer RNAs have been selected in vitro that bind to otherwise weakly fluorescent small molecules and enhance their fluorescence several thousand-fold. By genetically tagging cellular RNAs of interest with these aptamers and soaking cells in their cell-permeable cognate small-molecule fluorophores, it is possible to use them to study RNA localization and trafficking. These aptamers have also been fused to metabolite-binding RNAs to generate fluorescent biosensors. The 3D structures of three unrelated fluorogenic RNAs have been determined, and reveal a shared reliance on base quadruples (tetrads) to constrain the photo-excited chromophore. The structural diversity of fluorogenic RNAs and the chemical diversity of potential fluorophores to be activated are likely to yield a variety of future fluorogenic RNA tags that are optimized for different applications in RNA imaging and in the design of fluorescent RNA biosensors.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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9
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Khisamutdinov EF, Jasinski DL, Li H, Zhang K, Chiu W, Guo P. Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:10079-10087. [PMID: 27758001 PMCID: PMC5224701 DOI: 10.1002/adma.201603180] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/30/2016] [Indexed: 05/22/2023]
Abstract
Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, characterized by atomic force microscopy, cryo-electron microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis, is reported for the loading and protection of small molecules, proteins, small RNA molecules, and their controlled release.
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Affiliation(s)
- Emil F. Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Daniel L. Jasinski
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
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10
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Zhou Y, Chi H, Wu Y, Marks RS, Steele TWJ. Organic additives stabilize RNA aptamer binding of malachite green. Talanta 2016; 160:172-182. [PMID: 27591602 DOI: 10.1016/j.talanta.2016.06.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 11/27/2022]
Abstract
Aptamer-ligand binding has been utilized for biological applications due to its specific binding and synthetic nature. However, the applications will be limited if the binding or the ligand is unstable. Malachite green aptamer (MGA) and its labile ligand malachite green (MG) were found to have increasing apparent dissociation constants (Kd) as determined through the first order rate loss of emission intensity of the MGA-MG fluorescent complex. The fluorescent intensity loss was hypothesized to be from the hydrolysis of MG into malachite green carbinol base (MGOH). Random screening organic additives were found to reduce or retain the fluorescence emission and the calculated apparent Kd of MGA-MG binding. The protective effect became more apparent as the percentage of organic additives increased up to 10% v/v. The mechanism behind the organic additive protective effects was primarily from a ~5X increase in first order rate kinetics of MGOH→MG (kMGOH→MG), which significantly changed the equilibrium constant (Keq), favoring the generation of MG, versus MGOH without organic additives. A simple way has been developed to stabilize the apparent Kd of MGA-MG binding over 24h, which may be beneficial in stabilizing other triphenylmethane or carbocation ligand-aptamer interactions that are susceptible to SN1 hydrolysis.
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Affiliation(s)
- Yubin Zhou
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Hong Chi
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Yuanyuan Wu
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Robert S Marks
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore; Department of Biotechnology Engineering, Faculty of Engineering Sciences, Ben Gurion University of the NegevP.O. Box 653Beer Sheva84105Israel
| | - Terry W J Steele
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore.
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11
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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12
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Yin L, Wang W, Wang S, Zhang F, Zhang S, Tao N. How does fluorescent labeling affect the binding kinetics of proteins with intact cells? Biosens Bioelectron 2015; 66:412-6. [PMID: 25486538 PMCID: PMC4836836 DOI: 10.1016/j.bios.2014.11.036] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/25/2022]
Abstract
Fluorescent labeling is a mainstream technology for detecting molecular binding. Despite the importance, few studies have been devoted to quantitatively examine the effect of labeling on the molecular binding processes. Here we present a quantitative study on the binding kinetics of fluorescent-labeled and un-labeled molecules (lectin proteins) with glycoproteins on the membrane of cells using surface plasmon resonance imaging (SPRi) technique. The study shows that fluorescent labeling has a significant influence on the binding behaviors of proteins, especially the association processes, and the influence depends sensitively on the charge of fluorescent labels. It further shows that the labels also affect the local distribution of probe proteins, due to the inhomogeneous surface charge distribution of the cell membrane. Our work indicates that fluorescent labeling in general affects the binding behaviors, but proper design of the label will help to minimize its effect.
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Affiliation(s)
- Linliang Yin
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China; Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Shaopeng Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Fenni Zhang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shengtao Zhang
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
| | - Nongjian Tao
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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13
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Patra M, Mukhopadhyay C, Chakrabarti A. Malachite green interacts with the membrane skeletal protein, spectrin. RSC Adv 2015. [DOI: 10.1039/c5ra15488j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energy minimized complex of MG with the self association domain of spectrin.
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Affiliation(s)
- Malay Patra
- Chemistry Department
- University of Calcutta
- Kolkata 700009
- India
| | | | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
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14
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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15
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Han KY, Leslie BJ, Fei J, Zhang J, Ha T. Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging. J Am Chem Soc 2013; 135:19033-8. [PMID: 24286188 DOI: 10.1021/ja411060p] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of aptamer-fluorogen complexes is an emerging strategy for RNA imaging. Despite its promise for cellular imaging and sensing, the low fluorescence intensity of the Spinach-DFHBI RNA aptamer-fluorogen complex hampers its utility in quantitative live-cell and high-resolution imaging applications. Here we report that illumination of the Spinach-fluorogen complex induces photoconversion and subsequently fluorogen dissociation, leading to fast fluorescence decay and fluorogen-concentration-dependent recovery. The fluorescence lifetime of Spinach-DFHBI is 4.0 ± 0.1 ns irrespective of the extent of photoconversion. We detail a low-repetition-rate illumination scheme that enables us to maximize the potential of the Spinach-DFHBI RNA imaging tag in living cells.
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Affiliation(s)
- Kyu Young Han
- Howard Hughes Medical Institute , Urbana, Illinois 61801, United States
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16
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Ilgu M, Wang T, Lamm MH, Nilsen-Hamilton M. Investigating the malleability of RNA aptamers. Methods 2013; 63:178-87. [PMID: 23535583 DOI: 10.1016/j.ymeth.2013.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 10/27/2022] Open
Abstract
Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemical analysis with NMR spectroscopy and computational modeling to explore the relation between ligand binding and structural malleability of some well-studied aptamers. Several methods for determining aptamer binding affinity and specificity are discussed, including isothermal titration calorimetry, steady state fluorescence of 2-aminopurine substituted aptamers, and dye displacement assays. Also considered are aspects of molecular dynamics simulations specific to aptamers including adding ions and simulating aptamer structure in the absence of ligand when NMR spectroscopy or X-ray crystallography structures of the unoccupied aptamer are not available. We focus specifically on RNA aptamers that bind small molecule ligands as would be applied in sensors or integrated into riboswitches such as to measure the products of metabolic activity.
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Affiliation(s)
- Muslum Ilgu
- Ames Laboratory, US DOE, Ames, IA, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA, USA
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YANG XH, KONG WJ, YANG MH, ZHAO M, OUYANG Z. Application of Aptamer Identification Technology in Rapid Analysis of Mycotoxins. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60630-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Jia X, Li J, Wang E. Lighting-up of the dye malachite green with mercury(II)-DNA and its application for fluorescence turn-off detection of cysteine and glutathione. Chemistry 2012; 18:13494-500. [PMID: 22944915 DOI: 10.1002/chem.201103768] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 06/27/2012] [Indexed: 01/08/2023]
Abstract
This work describes a novel strategy for the highly sensitive and selective detection of cysteine (Cys) and glutathione (GSH) based on the Hg(2+)-AGRO100-malachite green (MG) complex system. The dye MG, which has a very low quantum yield in aqueous solution by itself, can bind with the thymine-rich DNA AGRO100 in the presence of Hg(2+) ions to generate a striking fluorescence intensity enhancement of 1000-fold. As sulfur-containing amino acids, Cys and GSH effectively sequester Hg(2+) ions from the Hg(2+)-AGRO100-MG complex structure to switch the 'lit-up' chemosensor to the 'off' state (about a 50-fold fluorescence intensity decrease), thus providing a facile, but effective, method to probe for Cys/GSH. The fluorescence titration, UV absorption, CD, and Raman spectra provide some insight into the structural and chemical basis for the enhancement effect. The formation of the Hg(2+)-AGRO100-MG complex significantly affects the electronic structure and conformation of the MG molecule by leading to an extended π system, which is the likely origin of the observed striking fluorescence intensity enhancement. Notably, the proposed sensing platform exhibits exquisite selectivity and sensitivity toward Cys/GSH with limits of detection of 5 nM for Cys and 10 nM for GSH, respectively. Furthermore, the straightforward assay design avoids labeling of the probe, uses only commercially available materials, and still displays comparable sensitivity and excellent selectivity.
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Affiliation(s)
- Xiaofang Jia
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
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Lux J, Peña EJ, Bolze F, Heinlein M, Nicoud JF. Malachite Green Derivatives for Two-Photon RNA Detection. Chembiochem 2012; 13:1206-13. [DOI: 10.1002/cbic.201100747] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Indexed: 11/09/2022]
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Lau JL, Baksh MM, Fiedler JD, Brown SD, Kussrow A, Bornhop DJ, Ordoukhanian P, Finn M. Evolution and protein packaging of small-molecule RNA aptamers. ACS NANO 2011; 5:7722-9. [PMID: 21899290 PMCID: PMC3209476 DOI: 10.1021/nn2006927] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A high-affinity RNA aptamer (K(d) = 50 nM) was efficiently identified by SELEX against a heteroaryldihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (nonencapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique.
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Affiliation(s)
- Jolene L. Lau
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael M. Baksh
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jason D. Fiedler
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven D. Brown
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Kussrow
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Darryl J. Bornhop
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Phillip Ordoukhanian
- Center for Protein and Nucleic Acid Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M.G. Finn
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Johnson PS, Cook PL, Liu X, Yang W, Bai Y, Abbott NL, Himpsel FJ. Universal mechanism for breaking amide bonds by ionizing radiation. J Chem Phys 2011; 135:044702. [DOI: 10.1063/1.3613638] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bernard Da Costa J, Dieckmann T. Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer. MOLECULAR BIOSYSTEMS 2011; 7:2156-63. [PMID: 21523267 DOI: 10.1039/c1mb05075c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of small molecule targets by RNA aptamers provides an excellent model to study the versatility of RNA function. The malachite green aptamer binds and recognizes its ligand via stacking and electrostatic interactions. The binding of the aptamer to its original selection target and three related molecules was determined by isothermal titration calorimetry, equilibrium dialysis, and fluorescence titration. The results reveal that the entropy of complex formation plays a large role in determining binding affinity and ligand specificity. These data combined with previous structural studies show that metal ions are required to stabilize the complexes with non-native ligands whereas the complex with the original selection target is stable at low salt and in the absence of divalent metal ions.
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Affiliation(s)
- Jason Bernard Da Costa
- University of Waterloo, Dept. of Chemistry, 200 University Ave West, Waterloo, ON, Canada
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Wang T, Hoy JA, Lamm MH, Nilsen-Hamilton M. Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity. J Am Chem Soc 2010; 131:14747-55. [PMID: 19778045 DOI: 10.1021/ja902719q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as "induced fit". But, it is not known to what extent this structural flexibility affects the integrity of the target-aptamer interaction. Using the malachite green aptamer (MGA) as a model system, we show that the MGA can protect its bound target, malachite green (MG), from oxidation over several days. Protection is reversed by an oligonucleotide complementary to the MGA binding pocket. Computational cavity analysis of the MGA-MG structure predicted that MG oxidation is protected because a molecule as small as an OH(-) is sterically excluded from the C1 position of the bound MG. These results suggest that, while the MGA-MG interface is sufficiently coherent to prevent OH(-) penetration, the bases involved in the interaction are sufficiently mobile that they can exchange out of the MG binding interface to hybridize with a complementary oligonucleotide. The computational predictions were confirmed experimentally using variants of the MGA with single base changes in the binding pocket. This work demonstrates the successful application of molecular dynamics simulations and cavity analysis in determining the effects of sequence variations on the structure of a small single-stranded nucleic acid. It also shows that a nucleic acid aptamer can control access to specific chemical groups on its target, which suggests that aptamers might be applied for selectively protecting small molecules from modification.
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Affiliation(s)
- Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Abstract
Bacterial ribosomal RNA is the target of clinically important antibiotics, while biologically important RNAs in viral and eukaryotic genomes present a range of potential drug targets. The physicochemical properties of RNA present difficulties for medicinal chemistry, particularly when oral availability is needed. Peptidic ligands and analysis of their RNA-binding properties are providing insight into RNA recognition. RNA-binding ligands include far more chemical classes than just aminoglycosides. Chemical functionalities from known RNA-binding small molecules are being exploited in fragment- and ligand-based projects. While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA–ligand interaction will be necessary to realize the full potential of this class of targets.
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Gilbert SD, Reyes FE, Edwards AL, Batey RT. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure 2009; 17:857-68. [PMID: 19523903 DOI: 10.1016/j.str.2009.04.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/01/2009] [Accepted: 04/02/2009] [Indexed: 12/30/2022]
Abstract
Purine riboswitches discriminate between guanine and adenine by at least 10,000-fold based on the identity of a single pyrimidine (Y74) that forms a Watson-Crick base pair with the ligand. To understand how this high degree of specificity for closely related compounds is achieved through simple pairing, we investigated their interaction with purine analogs with varying functional groups at the 2- and 6-positions that have the potential to alter interactions with Y74. Using a combination of crystallographic and calorimetric approaches, we find that binding these purines is often facilitated by either small structural changes in the RNA or tautomeric changes in the ligand. This work also reveals that, along with base pairing, conformational restriction of Y74 significantly contributes to nucleobase selectivity. These results reveal that compounds that exploit the inherent local flexibility within riboswitch binding pockets can alter their ligand specificity.
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Affiliation(s)
- Sunny D Gilbert
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
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27
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Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch. J Mol Graph Model 2009; 28:37-45. [PMID: 19380244 DOI: 10.1016/j.jmgm.2009.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 03/18/2009] [Accepted: 03/21/2009] [Indexed: 12/25/2022]
Abstract
Recent experimental study [S.D. Gilbert, S.J. Mediatore, R.T. Batey, Modified pyrimidine specifically bind the purine riboswitch, J. Am. Chem. Soc. 128 (2006) 14214-14215] demonstrated that the purine riboswitch could specifically bind some ligands other than purines such as amino-pyrimidines, and the authors proposed that the five-membered ring of purine was not required for recognition. To get insight into the interaction details, we used molecular docking method to investigate the interactions of a mutant form of guanine riboswitch with a series of amino-purines, amino-pyrimidines and imidazole derivatives, and employed molecular simulation method to study the dynamic behavior of the selected complexes. The calculation results reveal that (1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleobases including U22, U47, U51 and U74, which is consistent with the experimental results, while the two imidazole derivatives adopt other binding modes; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the number and position of amino substituents could seriously affect the binding of pyrimidines. As riboswitches are potentially excellent candidates for antibiotic therapeutics, these findings may be useful for understanding the range of compounds that riboswitch can specifically recognize.
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Afonin KA, Danilov EO, Novikova IV, Leontis NB. TokenRNA: a new type of sequence-specific, label-free fluorescent biosensor for folded RNA molecules. Chembiochem 2008; 9:1902-5. [PMID: 18655086 DOI: 10.1002/cbic.200800183] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kirill A Afonin
- Department of Chemistry ,Bowling Green State University, Bowling Green, OH 43403, USA
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Furukawa K, Abe H, Abe N, Harada M, Tsuneda S, Ito Y. Fluorescence generation from tandem repeats of a malachite green RNA aptamer using rolling circle transcription. Bioorg Med Chem Lett 2008; 18:4562-5. [PMID: 18667307 DOI: 10.1016/j.bmcl.2008.07.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 07/08/2008] [Accepted: 07/10/2008] [Indexed: 11/19/2022]
Abstract
We demonstrate a generation of tandem repeats of a malachite green (MG) RNA aptamer using rolling circle transcription. To keep the higher-order structure of each aptamer on long RNA, we designed a sequence of circular DNA with a 14-base linker. T7 RNA polymerase was superior to Escherichia coli RNA polymerase in the specific transcription of the MG RNA aptamer. Finally, the generation of the fluorescence signal was confirmed from aptamer repeats with MG.
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Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, Advanced Science Institute, RIKEN 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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Fluorinated analogs of malachite green: synthesis and toxicity. Molecules 2008; 13:986-94. [PMID: 18463600 PMCID: PMC6245195 DOI: 10.3390/molecules13040986] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 04/22/2008] [Accepted: 04/22/2008] [Indexed: 11/16/2022] Open
Abstract
A series of fluorinated analogs of malachite green (MG) have been synthesized and their toxicity to Saccharomyces cerevisiae and a human ovarian epithelial cell line examined. The toxicity profiles were found to be different for these two species. Two analogs, one with 2,4-difluoro substitution and the other with 2-fluoro substitution seem to be the most promising analogs because they showed the lowest toxicity to the human cells.
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31
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Bhasikuttan A, Mohanty J, Nau W, Pal H. Efficient Fluorescence Enhancement and Cooperative Binding of an Organic Dye in a Supra-biomolecular Host–Protein Assembly. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604757] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bhasikuttan AC, Mohanty J, Nau WM, Pal H. Efficient Fluorescence Enhancement and Cooperative Binding of an Organic Dye in a Supra-biomolecular Host–Protein Assembly. Angew Chem Int Ed Engl 2007; 46:4120-2. [PMID: 17443829 DOI: 10.1002/anie.200604757] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
The discovery of RNA-based catalysis 23 years ago dramatically changed the way biologists and biochemists thought of RNA. In the recent past, several ribozymes structures have provided some answers as to how catalysis is accomplished and how it relates to RNA structure and folding. However, there is still little information as to how catalytic activity evolved. Here we show that the small malachite green-binding aptamer has intrinsic catalytic potential that can be realized by designing the proper substrate. The charge distribution within the RNA binding pocket stabilizes the transition state of an ester hydrolysis reaction and thus accelerates the overall reaction. The results suggest that electrostatic forces can contribute significantly to RNA-based catalysis. Moreover, even simple RNA structures that have not been selected for catalytic properties can have a basic catalytic potential if they encounter the right substrate. This provides a possible starting point for the molecular evolution of more complex ribozymes.
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Affiliation(s)
- David M Brackett
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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Isaksson J, Plashkevych O, Pradeepkumar PI, Chatterjee S, Barman J, Pathmasiri W, Shrivastava P, Petit C, Chattopadhyaya J. Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study. J Biomol Struct Dyn 2005; 23:299-330. [PMID: 16218756 DOI: 10.1080/07391102.2005.10507067] [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: 10/28/2022]
Abstract
The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1',3'-O-anhydro-beta-D-psicofuranosyl) thymine, at the T(7) position of the self-complementary Dickerson-Drew dodecamer, d[(5'-C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12)-3')](2), considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and 1D NMR display a drop in melting temperature of approximately 10 degrees C per modification for the T(7) oxetane modified duplex, where the T(7) block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T(7) oxetane modified duplexes. The modified T(7) residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T(7).A(6) and A(6).T(7) non-linear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T(7) and T(8) residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T(7).A(6)/A(6).T(7) base pairs of the T(7) oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.
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Affiliation(s)
- J Isaksson
- Department of Bioorganic Chemistry, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden
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Sayer NM, Cubin M, Rhie A, Bullock M, Tahiri-Alaoui A, James W. Structural Determinants of Conformationally Selective, Prion-binding Aptamers. J Biol Chem 2004; 279:13102-9. [PMID: 14711834 DOI: 10.1074/jbc.m310928200] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have recently described the isolation of 2'-fluoropyrimidine-substituted RNA aptamers that bind selectively to disease-associated beta-sheet-rich forms of the prion protein, PrP, from a number of mammalian species. These aptamers inhibit the accumulation of protease-resistant forms of PrP in a prion-seeded, in vitro conversion assay. Here we identify the minimal portions of two of these aptamers that retain binding specificity. We determine their secondary structures by a combination of modeling and solution probing. Finally, we identify an internal site for biotinylation of a minimized, synthetic aptamer and use the resultant reagent in the detection of abnormal forms of PrP in vitro.
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Affiliation(s)
- Natalie M Sayer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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Flinders J, DeFina SC, Brackett DM, Baugh C, Wilson C, Dieckmann T. Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex. Chembiochem 2003; 5:62-72. [PMID: 14695514 DOI: 10.1002/cbic.200300701] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ribonucleic acids are an attractive drug target owing to their central role in many pathological processes. Notwithstanding this potential, RNA has only rarely been successfully targeted with novel drugs. The difficulty of targeting RNA is at least in part due to the unusual mode of binding found in most small-molecule-RNA complexes: the ligand binding pocket of the RNA is largely unstructured in the absence of ligand and forms a defined structure only with the ligand acting as scaffold for folding. Moreover, electrostatic interactions between RNA and ligand can also induce significant changes in the ligand structure due to the polyanionic nature of the RNA. Aptamers are ideal model systems to study these kinds of interactions owing to their small size and the ease with which they can be evolved to recognize a large variety of different ligands. Here we present the solution structure of an RNA aptamer that binds triphenyl dyes in complex with malachite green and compare it with a previously determined crystal structure of a complex formed with tetramethylrosamine. The structures illustrate how the same RNA binding pocket can adapt to accommodate both planar and nonplanar ligands. Binding studies with single- and double-substitution mutant aptamers are used to correlate three-dimensional structure with complex stability. The two RNA-ligand complex structures allow a discussion of structural changes that have been observed in the ligand in the context of the overall complex structure. Base pairing and stacking interactions within the RNA fold the phosphate backbone into a structure that results in an asymmetric charge distribution within the binding pocket that forces the ligand to adapt through a redistribution of the positive partial charge.
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Affiliation(s)
- Jeremy Flinders
- Department of Chemistry, University of California, Davis, CA 95616, USA
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