1
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Saha R, Kao WL, Malady B, Heng X, Chen IA. Effect of montmorillonite K10 clay on RNA structure and function. Biophys J 2024; 123:451-463. [PMID: 37924206 PMCID: PMC10912936 DOI: 10.1016/j.bpj.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 09/29/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
One of the earliest living systems was likely based on RNA ("the RNA world"). Mineral surfaces have been postulated to be an important environment for the prebiotic chemistry of RNA. In addition to adsorbing RNA and thus potentially reducing the chance of parasitic takeover through limited diffusion, minerals have been shown to promote a range of processes related to the emergence of life, including RNA polymerization, peptide bond formation, and self-assembly of vesicles. In addition, self-cleaving ribozymes have been shown to retain activity when adsorbed to the clay mineral montmorillonite. However, simulation studies suggest that adsorption to minerals is likely to interfere with RNA folding and, thus, function. To further evaluate the plausibility of a mineral-adsorbed RNA world, here we studied the effect of the synthetic clay montmorillonite K10 on the malachite green RNA aptamer, including binding of the clay to malachite green and RNA, as well as on the formation of secondary structures in model RNA and DNA oligonucleotides. We evaluated the fluorescence of the aptamer complex, adsorption to the mineral, melting curves, Förster resonance energy transfer interactions, and 1H-NMR signals to study the folding and functionality of these nucleic acids. Our results indicate that while some base pairings are unperturbed, the overall folding and binding of the malachite green aptamer are substantially disrupted by montmorillonite. These findings suggest that minerals would constrain the structures, and possibly the functions, available to an adsorbed RNA world.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Wei-Ling Kao
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Brandon Malady
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California.
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2
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Chen K, Zhu L, Du Z, Lan X, Huang K, Zhang W, Xu W. Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130798. [PMID: 36669418 DOI: 10.1016/j.jhazmat.2023.130798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Although nucleic acid aptasensors are increasingly applied in the detection of environmentally hazardous biomolecules, several formidable challenges remain with this technique because of their vulnerability, high cost and suboptimal sensitivity. Here, a docking-aided rational tailoring (DART) strategy was established at three levels and in two dimensions for the refinement of malachite green (MG) DNA aptamers. Guided by in silico molecular docking, coarse and fine tailoring were conducted at three levels each, to significantly enhance fluorescence activation intensity and binding affinity in two dimensions. Empowered by the results of the rational tailoring, a mechanistic view of the MG DNA aptamer-target interaction was thoroughly analyzed via four types of interactions. To meet the demand for point-of-care testing (POCT), a label-free and ratiometric fluorescent aptasensor was developed leveraging the tailored MG aptamer, based on the binding site competition-equilibrium effect via the introduction of a reference dye. This sensitive, specific, low-cost and rapid aptasensor subsequently demonstrated outstanding detection performance, achieving an ideal signal response range of 5 nmol·L-1 - 6 μmol·L-1 and a low limit of detection (LOD) of 1.49 nmol·L-1. The DART strategy and systematic exploration of the MG DNA luminescent aptamers herein will provide a valuable reference in the field of aptamer tailoring, biosensing and bioimaging. The proposed label-free ratiometric aptasensor also provides a highly generalizable strategy for hazardous biomolecular detection.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Zaihui Du
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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3
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Endoh T, Tan JH, Chen SB, Sugimoto N. Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells. Anal Chem 2023; 95:976-985. [PMID: 36541622 DOI: 10.1021/acs.analchem.2c03598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent successes in construction of light-up RNA aptamers allowed fluorescence-based live-cell imaging of RNAs. In addition, light-up aptamers have been converted into signaling aptamers that enable fluorometric detection of small chemicals. To date, only a single target chemical has been detected at a time in cells. In this study, we selected cladogenetic orthogonal light-up aptamers that output three different colors from the RNA library having the same ligand binding core. Two of the three functioned in mammalian cells. These two aptamers, which fluoresce blue and green upon binding of cognate fluorogen, were converted into signaling aptamers. Using these signaling aptamers in combination with a previously described light-up aptamer with red fluorescence, we demonstrated simultaneous detection of multiple chemicals in living cells. The cladogenetic orthogonal light-up aptamers developed in this study and the simple strategy for rational designing of the signaling aptamers will provide innovative advances in the field of RNA-based bioimaging.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou510006, China
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan
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4
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Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
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Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
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5
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Zerze GH, Piaggi PM, Debenedetti PG. A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States. J Phys Chem B 2021; 125:13685-13695. [PMID: 34890201 DOI: 10.1021/acs.jpcb.1c08038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important characteristic of RNA folding is the adoption of alternative configurations of similar stability, often referred to as misfolded configurations. These configurations are considered to compete with correctly folded configurations, although their rigorous thermodynamic and structural characterization remains elusive. Tetraloop motifs found in large ribozymes are ideal systems for an atomistically detailed computational quantification of folding free energy landscapes and the structural characterization of their constituent free energy basins, including nonnative states. In this work, we studied a group of closely related 10-mer tetraloops using a combined parallel tempering and metadynamics technique that allows a reliable sampling of the free energy landscapes, requiring only knowledge that the stem folds into a canonical A-RNA configuration. We isolated and analyzed unfolded, folded, and misfolded populations that correspond to different free energy basins. We identified a distinct misfolded state that has a stability very close to that of the correctly folded state. This misfolded state contains a predominant population that shares the same structural features across all tetraloops studied here and lacks the noncanonical A-G base pair in its loop portion. Further analysis performed with biased trajectories showed that although this competitive misfolded state is not an essential intermediate, it is visited in most of the transitions from unfolded to correctly folded states. Moreover, the tetraloops can transition from this misfolded state to the correctly folded state without requiring extensive unfolding.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo M Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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6
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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7
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Rekand IH, Brenk R. DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. J Chem Inf Model 2021; 61:4068-4081. [PMID: 34286972 PMCID: PMC8389535 DOI: 10.1021/acs.jcim.1c00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
RNA is an emerging
target for drug discovery. However, like for
proteins, not all RNA binding sites are equally suited to be addressed
with conventional drug-like ligands. To this end, we have developed
the structure-based druggability predictor DrugPred_RNA to identify
druggable RNA binding sites. Due to the paucity of annotated RNA binding
sites, the predictor was trained on protein pockets, albeit using
only descriptors that can be calculated for both RNA and protein binding
sites. DrugPred_RNA performed well in discriminating druggable from
less druggable binding sites for the protein set and delivered predictions
for selected RNA binding sites that agreed with manual assignment.
In addition, most drug-like ligands contained in an RNA test set were
found in pockets predicted to be druggable, further adding confidence
to the performance of DrugPred_RNA. The method is robust against conformational
and sequence changes in the binding sites and can contribute to direct
drug discovery efforts for RNA targets.
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Affiliation(s)
- Illimar Hugo Rekand
- Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway
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8
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Piccolo KA, McNeil B, Crouse J, Lim SJ, Bickers SC, Hopkins WS, Dieckmann T. Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer. Biochem Biophys Res Commun 2020; 529:666-671. [PMID: 32736690 DOI: 10.1016/j.bbrc.2020.06.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 10/23/2022]
Abstract
Binding affinity and selectivity are critical properties of aptamers that must be optimized for any application. The sulforhodamine B binding RNA aptamer (SRB-2) is a somewhat promiscuous aptamer that can bind ligands that vary markedly in shape, size and charge. Here we categorize potential ligands based on their binding mode and structural characteristics required for high affinity and selectivity. Several known and potential ligands of SRB-2 were screened for binding affinity using LSPR, ITC and NMR spectroscopy. The study shows that rhodamine B has the ideal structural and electrostatic properties for selective and high-affinity binding of the SRB-2 aptamer.
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Affiliation(s)
- Kyle A Piccolo
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Brooke McNeil
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jeff Crouse
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Su Ji Lim
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah C Bickers
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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9
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Bu S, Jiang G, Jiang G, Liu J, Lin X, Shen J, Xiong Y, Duan X, Wang J, Liao X. Antibacterial activity of ruthenium polypyridyl complexes against Staphylococcus aureus and biofilms. J Biol Inorg Chem 2020; 25:747-757. [PMID: 32564223 DOI: 10.1007/s00775-020-01797-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 12/29/2022]
Abstract
There is clearly a need for the development of new classes of antimicrobials to fight against multidrug-resistant bacteria. Here, we designed and synthesized of three ruthenium polypyridyl complexes: [Ru(bpy)2(BTPIP)](ClO4)2 (Ru(II)-1), [Ru(bpy)2(ETPIP)](ClO4)2 (Ru(II)-2) and [Ru(bpy)2(CAPIP)](ClO4)2 (Ru(II)-3) (N-N = bpy = 2,2'-bipyridine), their antimicrobial activities against S. aureus were assessed. The lead complexes of this set, Ru(II)-1(MIC = 0.016 mg/mL), was tested against biofilm. We also investigated whether bacteria can easily develop resistance to Ru(II)-1. The result demonstrated that S. aureus could not easily develop resistance to the ruthenium complexes. In addition, aimed to test whether ruthenium complexes treatment could increase the susceptibility of S. aureus to antibiotics, the synergism between Ru(II)-1 and common antibiotics against S. aureus were investigated using the checkerboard method. Interesting, Ru(II)-1 could increased the susceptibility of S. aureus to some aminoglycoside antibiotics(kanamycin and gentamicin). Finally, in vivo bacterial infection treatment studies were also conducted through murine skin infection model. These results confirmed ruthenium complexes have good antimicrobial activity in vitro and in vivo.
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Affiliation(s)
- Simeng Bu
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Guijuan Jiang
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Guangbin Jiang
- Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China
| | - Jinyao Liu
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Xiaoli Lin
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Jihong Shen
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Yanshi Xiong
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Xuemin Duan
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Jintao Wang
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
| | - Xiangwen Liao
- School of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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10
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Liao X, Jiang G, Wang J, Duan X, Liao Z, Lin X, Shen J, Xiong Y, Jiang G. Two ruthenium polypyridyl complexes functionalized with thiophen: synthesis and antibacterial activity against Staphylococcus aureus. NEW J CHEM 2020. [DOI: 10.1039/d0nj02944k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ruthenium polypyridyl complex Ru(ii)-2 could increase the susceptibility of S. aureus to the aminoglycoside antibiotic (kanamycin).
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Affiliation(s)
- Xiangwen Liao
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Guijuan Jiang
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Jintao Wang
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Xuemin Duan
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Zhouyuji Liao
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Xiaoli Lin
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Jihong Shen
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Yanshi Xiong
- School of Pharmacy
- Jiangxi Science & Technology Normal University
- Nanchang
- China
| | - Guangbin Jiang
- Guangxi Key Laboratory of Electrochemical and Magneto-chemical Function Materials
- College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin
- China
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11
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Saha R, Chen IA. Effect of UV Radiation on Fluorescent RNA Aptamers' Functional and Templating Ability. Chembiochem 2019; 20:2609-2617. [PMID: 31125512 PMCID: PMC6899979 DOI: 10.1002/cbic.201900261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Indexed: 12/25/2022]
Abstract
Damage from ultraviolet (UV) radiation was likely to be an important selection pressure during the origin of life. RNA is believed to have been central to the origin of life and might form the basis for simple synthetic cells. Although photodamage of DNA has been extensively studied, photodamage is highly dependent on local molecular context, and damage to functional RNAs has been relatively under‐studied. We irradiated two fluorescent RNA aptamers and monitored the loss of activity, folding, and the kinetics of lesion accumulation. The loss of activity differed depending on the aptamer, with the Spinach2 aptamer retaining substantial activity after long exposure times. The binding pocket was particularly susceptible to damage, and melting of the duplex regions increased susceptibility; this is consistent with the view that duplex formation is protective. At the same time, susceptibility varied greatly depending on context, thus emphasizing the importance of studying many different RNAs to understand UV hardiness.
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Affiliation(s)
- Ranajay Saha
- Department of Chemistry and Biochemistry, 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.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
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12
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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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13
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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14
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Sengupta RN, Herschlag D. Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry 2019; 58:2760-2768. [PMID: 31117387 PMCID: PMC6586055 DOI: 10.1021/acs.biochem.9b00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The diverse biological
processes mediated by RNA rest upon its
recognition of various ligands, including small molecules and nucleic
acids. Nevertheless, a recent literature survey suggests that RNA
molecular recognition of these ligands is slow, with association rate
constants orders of magnitude below the diffusional limit. Thus, we
were prompted to consider strategies for increasing RNA association
kinetics. Proteins can accelerate ligand association via electrostatic
forces, and here, using the Tetrahymena group I ribozyme,
we provide evidence that electrostatic forces can accelerate RNA/ligand
association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide
substrate (S) by an exogenous guanosine (G) cofactor. The G 2′-
and 3′-OH groups interact with an active site metal ion, termed
MC, within E·S·G, and we perturbed each of these
contacts via −NH3+ substitution. New
and prior data indicate that G(2′NH3+) and G(3′NH3+) bind as strongly as
G, suggesting that the −NH3+ substituents
of these analogues avoid repulsive interactions with MC and make alternative interactions. Unexpectedly, removal of the
adjacent −OH via −H substitution to give G(2′H,3′NH3+) and G(2′NH3+,3′H) enhanced binding, in stark contrast to the deleterious
effect of these substitutions on G binding. Pulse–chase experiments
indicate that the −NH3+ moiety of G(2′H,3′NH3+) increases the rate of G association. These results
suggest that the positively charged −NH3+ group can act as a molecular “anchor” to increase
the residence time of the encounter complex and thereby enhance productive
binding. Electrostatic anchors may provide a broadly applicable strategy
for the development of fast binding RNA ligands and RNA-targeted therapeutics.
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Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel Herschlag
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States.,Departments of Chemical Engineering and Chemistry , Stanford University , Stanford , California 94305 , United States.,Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health) , Stanford University , Stanford , California 94305 , United States
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15
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Belinskaia DA, Avdonin PV, Avdonin PP, Jenkins RO, Goncharov NV. Rational in silico design of aptamers for organophosphates based on the example of paraoxon. Comput Biol Chem 2019; 80:452-462. [PMID: 31170561 DOI: 10.1016/j.compbiolchem.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 01/20/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its three-dimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.
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Affiliation(s)
- Daria A Belinskaia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, St. Petersburg 194223, Russia.
| | - Pavel V Avdonin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Piotr P Avdonin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Richard O Jenkins
- Leicester School of Allied Health Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Nikolay V Goncharov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, St. Petersburg 194223, Russia; Research Institute of Hygiene, Occupational Pathology and Human Ecology, bld.93 p.o.Kuz'molovsky, Leningrad Region 188663, Russia
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16
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Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun 2018; 9:4542. [PMID: 30382099 PMCID: PMC6208384 DOI: 10.1038/s41467-018-06942-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022] Open
Abstract
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.
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Affiliation(s)
- Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Artur Laski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaohong Tan
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tudor P Constantin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Alan S Waggoner
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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17
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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18
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Identification of small-molecule ligands that bind to MiR-21 as potential therapeutics for endometriosis by screening ZINC database and in-vitro assays. Gene 2018; 662:46-53. [DOI: 10.1016/j.gene.2018.03.094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/17/2018] [Accepted: 03/28/2018] [Indexed: 12/20/2022]
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19
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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: 41] [Impact Index Per Article: 6.8] [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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20
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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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21
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Jasinski D, Haque F, Binzel DW, Guo P. Advancement of the Emerging Field of RNA Nanotechnology. ACS NANO 2017; 11:1142-1164. [PMID: 28045501 PMCID: PMC5333189 DOI: 10.1021/acsnano.6b05737] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/03/2017] [Indexed: 05/14/2023]
Abstract
The field of RNA nanotechnology has advanced rapidly during the past decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) developing methods to control shape, size, and stoichiometry of RNA nanoparticles; (6) increasing knowledge of regulation and processing functions of RNA in cells; (7) decreasing cost of RNA production by biological and chemical synthesis; and (8) proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs. Other applications of RNA nanotechnology, such as adapting them to construct 2D, 3D, and 4D structures for use in tissue engineering, biosensing, resistive biomemory, and potential computer logic gate modules, have stimulated the interest of the scientific community. This review aims to outline the current state of the art of RNA nanoparticles as programmable smart complexes and offers perspectives on the promising avenues of research in this fast-growing field.
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Affiliation(s)
| | | | - Daniel W Binzel
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
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22
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Li H, Zhang K, Pi F, Guo S, Shlyakhtenko L, Chiu W, Shu D, Guo P. Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:7501-7. [PMID: 27322097 PMCID: PMC5059845 DOI: 10.1002/adma.201601976] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Indexed: 05/20/2023]
Abstract
RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy.
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Affiliation(s)
- Hui Li
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaiming Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fengmei Pi
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Sijin Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Luda Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Shu
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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23
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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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24
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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25
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Sengupta RN, Van Schie SNS, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. RNA (NEW YORK, N.Y.) 2016; 22:32-48. [PMID: 26567314 PMCID: PMC4691833 DOI: 10.1261/rna.053710.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function.
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Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Sabine N S Van Schie
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - George Giambaşu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph D Yesselman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Darrin York
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA Department of Chemical Engineering, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA
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26
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Berens C, Groher F, Suess B. RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression. Biotechnol J 2015; 10:246-57. [PMID: 25676052 DOI: 10.1002/biot.201300498] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/23/2014] [Accepted: 01/15/2015] [Indexed: 12/16/2022]
Abstract
RNA utilizes many different mechanisms to control gene expression. Among the regulatory elements that respond to external stimuli, riboswitches are a prominent and elegant example. They consist solely of RNA and couple binding of a small molecule ligand to the so-called "aptamer domain" with a conformational change in the downstream "expression platform" which then determines system output. The modular organization of riboswitches and the relative ease with which ligand-binding RNA aptamers can be selected in vitro against almost any molecule have led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology over the past decade. This review highlights proof-of-principle applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression in pro- and eukaryotes. It then focuses on strategies and parameters to identify aptamers that can be integrated into synthetic riboswitches that are functional in vivo, before finishing with a reflection on how to improve the regulatory properties of engineered riboswitches, so that we can not only further expand riboswitch applicability, but also finally fully exploit their potential as control elements in regulating gene expression.
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Affiliation(s)
- Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
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27
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Duchardt-Ferner E, Weigand JE, Ohlenschläger O, Schmidtke SR, Suess B, Wöhnert J. Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch. Angew Chem Int Ed Engl 2015; 49:6216-9. [PMID: 20632338 DOI: 10.1002/anie.201001339] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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28
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Adamala K, Engelhart AE, Szostak JW. Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension. J Am Chem Soc 2014; 137:483-9. [PMID: 25521912 PMCID: PMC4984999 DOI: 10.1021/ja511564d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The earliest genomic RNAs had to
be short enough for efficient
replication, while simultaneously serving as unfolded templates and
effective ribozymes. A partial solution to this paradox may lie in
the fact that many functional RNAs can self-assemble from multiple
fragments. Therefore, in early evolution, genomic RNA fragments could
have been significantly shorter than unimolecular functional RNAs.
Here, we show that unstable, nonfunctional complexes assembled from
even shorter 3′-truncated oligonucleotides can be stabilized
and gain function via non-enzymatic primer extension. Such short RNAs
could act as good templates due to their minimal length and complex-forming
capacity, while their minimal length would facilitate replication
by relatively inefficient polymerization reactions. These RNAs could
also assemble into nascent functional RNAs and undergo conversion
to catalytically active forms, by the same polymerization chemistry
used for replication that generated the original short RNAs. Such
phenomena could have substantially relaxed requirements for copying
efficiency in early nonenzymatic replication systems.
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Affiliation(s)
- Katarzyna Adamala
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States
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Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e201. [PMID: 25291143 PMCID: PMC4217074 DOI: 10.1038/mtna.2014.49] [Citation(s) in RCA: 341] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.
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Papper V, Pokholenko O, Wu Y, Zhou Y, Jianfeng P, Steele TWJ, Marks RS. Novel Photochrome Aptamer Switch Assay (PHASA) for adaptive binding to aptamers. J Fluoresc 2014; 24:1581-91. [PMID: 25187086 DOI: 10.1007/s10895-014-1441-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
A novel Photochrome-Aptamer Switch Assay (PHASA) for the detection and quantification of small environmentally important molecules such as toxins, explosives, drugs and pollutants, which are difficult to detect using antibodies-based assays with high sensitivity and specificity, has been developed. The assay is based on the conjugation of a particular stilbene-analyte derivative to any aptamer of interest. A unique feature of the stilbene molecule is its reporting power via trans-cis photoisomerisation (from fluorescent trans-isomer to non-fluorescent cis-isomer) upon irradiation with the excitation light. The resulting fluorescence decay rate for the trans-isomer of the stilbene-analyte depends on viscosity and spatial freedom to rotate in the surrounding medium and can be used to indicate the presence of the analyte. Quantification of the assay is achieved by calibration of the fluorescence decay rate for the amount of the tested analyte. Two different formats of PHASA have been recently developed: direct conjugation and adaptive binding. New stilbene-maleimide derivatives used in the adaptive binding format have been prepared and characterised. They demonstrate effective binding to the model thiol compound and to the thiolated Malachite Green aptamer.
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Affiliation(s)
- Vladislav Papper
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
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31
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Wang YQ, Zhang HM, Cao J. Exploring the interactions of decabrominateddiphenyl ether and tetrabromobisphenol A with human serum albumin. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 38:595-606. [PMID: 25194328 DOI: 10.1016/j.etap.2014.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 06/03/2023]
Abstract
Decabrominateddiphenyl ether (deca-BDE) and tetrabromobisphenol A (TBBPA) are known as brominated flame-retardants, which are commonly found in the environment. The binding mechanisms of deca-BDE and TBBPA with human serum albumin (HSA) are still unknown. In this report, the interactions of deca-BDE and TBBPA with HSA were investigated using different spectroscopic methods and molecular modeling. The experimental results indicated the formation of complexes between deca-BDE/TBBPA and HSA with different affinity. These interactions affected the secondary structure of HSA. Thermodynamic investigations revealed that hydrophobic forces mainly drove the binding interactions of deca-BDE/TBBPA with HSA. For TBBPA, hydrogen-bonding interactions were also involved in the binding process of TBBPA with HSA. According to the analysis of experimental and theoretical data, we concluded that the binding site of deca-BDE to HSA located in the subdomain IB, while TBBPA was near to subdomain IIA and Trp-214. The binding interactions of deca-BDE and TBBPA with the most prominent carrier protein in the human circulatory system could influence mechanisms of their biochemical processes. Thus, these binding interactions can play central roles in studying the distribution and toxicity mechanisms of brominated flame-retardants.
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Affiliation(s)
- Yan-Qing Wang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China.
| | - Hong-Mei Zhang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China
| | - Jian Cao
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China
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32
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Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferré-D’Amaré AR. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 2014; 21:658-63. [PMID: 25026079 PMCID: PMC4143336 DOI: 10.1038/nsmb.2865] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/07/2014] [Indexed: 12/22/2022]
Abstract
GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.
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Affiliation(s)
| | - Michael C. Chen
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
| | - Rita L. Strack
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
| | - Andrea Thorn
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
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33
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Nucleic acid aptamers: research tools in disease diagnostics and therapeutics. BIOMED RESEARCH INTERNATIONAL 2014; 2014:540451. [PMID: 25050359 PMCID: PMC4090538 DOI: 10.1155/2014/540451] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
Abstract
Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.
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Szeitner Z, András J, Gyurcsányi RE, Mészáros T. Is less more? Lessons from aptamer selection strategies. J Pharm Biomed Anal 2014; 101:58-65. [PMID: 24877649 DOI: 10.1016/j.jpba.2014.04.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 12/19/2022]
Abstract
Aptamers have many inherent advantages originating from their in vitro selection and tailored chemical synthesis that makes them appealing alternatives of antibodies in bioaffinity assays. However, what ultimately matters, and that is the prerequisite to give way to all these advantages, is how well, and how selectively the aptamers bind to their targets. With the aptamer selection largely in the hand of life scientists, analytical chemists focused mostly on methodological development of aptamer-based assays using a fairly restricted number of aptamers to prove their concepts. However, ideally the development of an aptamer-based assay should start from the selection of aptamers to ensure their proper functionality in real samples. For instance information on the sample matrix can be implemented within counter-selection steps to discard aptamer candidates that show cross-reactivity to matrix components or critical interferents. In general, a larger consideration of the analytical use during selection and characterization of aptamers have been shown to increase the applicability of aptamers. Therefore, this review is a short, subjective view on trends in aptamer development highlighting factors to consider during their selection for a successful analytical application.
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Affiliation(s)
- Zsuzsanna Szeitner
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| | - Judit András
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary; MTA-BME Technical Analytical Chemistry Research Group of the Hungarian Academy of Sciences, Szent Gellért tér 4, H-1111 Budapest, Hungary.
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35
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Da Costa JB, Andreiev AI, Dieckmann T. Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer. Biochemistry 2013; 52:6575-83. [PMID: 23984874 DOI: 10.1021/bi400549s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. The malachite green aptamer (MGA) has been shown to bind several closely related triphenyl dyes with planar and nonplanar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA-ligand interaction. The results of these studies reveal that binding of one ligand can reduce the ability of the aptamer pocket to adapt to another ligand, even if this second ligand has a significantly higher affinity to the free aptamer. A similar effect is observed in the presence of Mg(2+) ions which stabilize the binding pocket in a more ligand bound-like conformation.
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Affiliation(s)
- Jason B Da Costa
- Department of Chemistry, University of Waterloo , 200 University Ave West, Waterloo, ON N2L3G1, Canada
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36
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Appasamy SD, Ramlan EI, Firdaus-Raih M. Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches. PLoS One 2013; 8:e73984. [PMID: 24040136 PMCID: PMC3764141 DOI: 10.1371/journal.pone.0073984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 07/25/2013] [Indexed: 12/17/2022] Open
Abstract
The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.
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Affiliation(s)
- Sri D Appasamy
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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37
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Szent-Gyorgyi C, Stanfield RL, Andreko S, Dempsey A, Ahmed M, Capek S, Waggoner AS, Wilson IA, Bruchez MP. Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces. J Mol Biol 2013; 425:4595-613. [PMID: 23978698 DOI: 10.1016/j.jmb.2013.08.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 01/19/2023]
Abstract
We report that a symmetric small-molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* fluorogen activating protein is a VL domain that binds malachite green (MG) dye to activate intense fluorescence. Crystallography of liganded L5* reveals a 2:1 protein:ligand complex with inclusive C2 symmetry, where MG is almost entirely encapsulated between an antiparallel arrangement of the two VL domains. Unliganded L5* VL domains crystallize as a similar antiparallel VL/VL homodimer. The complementarity-determining regions are spatially oriented to form novel VL/VL and VL/ligand interfaces that tightly constrain a propeller conformer of MG. Binding equilibrium analysis suggests highly cooperative assembly to form a very stable VL/MG/VL complex, such that MG behaves as a strong chemical inducer of dimerization. Fusion of two VL domains into a single protein tightens MG binding over 1000-fold to low picomolar affinity without altering the large binding enthalpy, suggesting that bonding interactions with ligand and restriction of domain movements make independent contributions to binding. Fluorescence activation of a symmetrical fluorogen provides a selection mechanism for the isolation and directed evolution of ternary complexes where unnatural symmetric binding interfaces are favored over canonical antibody interfaces. As exemplified by L5*, these self-reporting complexes may be useful as modulators of protein association or as high-affinity protein tags and capture reagents.
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Affiliation(s)
- Chris Szent-Gyorgyi
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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38
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Schill M, Koslowski T. Sensing organic molecules by charge transfer through aptamer-target complexes: theory and simulation. J Phys Chem B 2013; 117:475-83. [PMID: 23227783 DOI: 10.1021/jp308042n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aptamers, i.e., short sequences of RNA and single-stranded DNA, are capable of specificilly binding objects ranging from small molecules over proteins to entire cells. Here, we focus on the structure, stability, dynamics, and electronic properties of oligonucleotides that interact with aromatic or heterocyclic targets. Large-scale molecular dynamics simulations indicate that aromatic rings such as dyes, metabolites, or alkaloides form stable adducts with their oligonucleotide host molecules at least on the simulation time scale. From molecular dynamics snapshots, the energy parameters relevant to Marcus' theory of charge transfer are computed using a modified Su-Schrieffer-Heeger Hamiltonian, permitting an estimate of the charge transfer rates. In many cases, aptamer binding seriously influences the charge transfer kinetics and the charge carrier mobility within the complex, with conductivities up to the nanoampere range for a single complex. We discuss the conductivity properties with reference to potential applications as biosensors.
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Affiliation(s)
- Maria Schill
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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39
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Sathish V, Babu E, Ramdass A, Lu ZZ, Chang TT, Velayudham M, Thanasekaran P, Lu KL, Li WS, Rajagopal S. Photoswitchable alkoxy-bridged binuclear rhenium(i) complexes – a potential probe for biomolecules and optical cell imaging. RSC Adv 2013. [DOI: 10.1039/c3ra42627k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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40
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 283] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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41
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Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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42
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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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Meng L, Yang L, Zhao X, Zhang L, Zhu H, Liu C, Tan W. Targeted delivery of chemotherapy agents using a liver cancer-specific aptamer. PLoS One 2012; 7:e33434. [PMID: 22558072 PMCID: PMC3338807 DOI: 10.1371/journal.pone.0033434] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/08/2012] [Indexed: 11/18/2022] Open
Abstract
Background Using antibody/aptamer-drug conjugates can be a promising method for decreasing toxicity, while increasing the efficiency of chemotherapy. Methodology/Principal Findings In this study, the antitumor agent Doxorubicin (Dox) was incorporated into the modified DNA aptamer TLS11a-GC, which specifically targets LH86, a human hepatocellular carcinoma cell line. Cell viability tests demonstrated that the TLS11a-GC-Dox conjugates exhibited both potency and target specificity. Importantly, intercalating Dox into the modified aptamer inhibited nonspecific uptake of membrane-permeable Dox to the non-target cell line. Since the conjugates are selective for cells that express higher amounts of target proteins, both criteria noted above are met, making TLS11a-GC-Dox conjugates potential candidates for targeted delivery to liver cancer cells. Conclusions/Significance Considering the large number of available aptamers that have specific targets for a wide variety of cancer cells, this novel aptamer-drug intercalation method will have promising implications for chemotherapeutics in general.
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Affiliation(s)
- Ling Meng
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Liu Yang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Xiangxuan Zhao
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Lucy Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Haizhen Zhu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, People’s Republic of China
| | - Chen Liu
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (WT); (CL)
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (WT); (CL)
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Xu W, Xiang Y, Ihms H, Lu Y. Label-Free Fluorescent Sensors Based on Functional Nucleic Acids. REVIEWS IN FLUORESCENCE 2010 2012. [DOI: 10.1007/978-1-4419-9828-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sokoloski JE, Dombrowski SE, Bevilacqua PC. Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer. Biochemistry 2011; 51:565-72. [PMID: 22192051 DOI: 10.1021/bi201642p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The malachite green aptamer binds two closely related ligands, malachite green (MG) and tetramethylrosamine (TMR), with nearly equal affinity. The MG ligand consists of three phenyl rings emanating from a central carbon, while TMR has two of the three rings connected by an ether linkage. The binding pockets for MG and TMR in the aptamer, known from high-resolution structures, differ only in the conformation of a few nucleotides. Herein, we applied isothermal titration calorimetry (ITC) to compare the thermodynamics of binding of MG and TMR to the aptamer. Binding heat capacities were obtained from ITC titrations over the temperature range of 15-60 °C. Two temperature regimes were found for MG binding: one from 15 to 45 °C where MG bound with a large negative heat capacity and an apparent stoichiometry (n) of ~0.4 and another from 50 to 60 °C where MG bound with a positive heat capacity and an n of ~1.1. The binding of TMR, on the other hand, revealed only one temperature regime for binding, with a more modest negative heat capacity and an n of ~1.2. The large difference in heat capacity between the two ligands suggests that significantly more conformational rearrangement occurs upon the binding of MG than that of TMR, which is consistent with differences in solvent accessible surface area calculated for available ligand-bound structures. Lastly, we note that the binding stoichiometry of MG was improved not only by an increase in the temperature but also by a decrease in the concentration of Mg(2+) or an increase in the time between ITC injections. These studies suggest that binding of a dynamical ligand to a functional RNA requires the RNA itself to have significant dynamics.
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Affiliation(s)
- Joshua E Sokoloski
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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47
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Zhu G, Lübbecke M, Walter JG, Stahl F, Scheper T. Characterization of Optimal Aptamer-Microarray Binding Chemistry and Spacer Design. Chem Eng Technol 2011. [DOI: 10.1002/ceat.201000551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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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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Abelow AE, White RJ, Plaxco KW, Zharov I. Nanoporous silica colloidal films with molecular transport gated by aptamers responsive to small molecules. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report the preparation of colloidal nanoporous silica films whose function mimics that of protein channels in gating the transport of small molecules across a cell membrane. Specifically, we report a means of controlling the molecular flux through colloidal nanopores that employ aptamer oligonucleotides binding to a specific organic small molecule (cocaine). These biomacromolecules have been introduced onto the nanopore surface by attaching pre-made oligonucleotides to the activated nanopore surface. The aptamers change their conformation in response to the binding events, and thus alter the free volume of the colloidal nanopores available for molecular transport.
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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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