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Uda RM, Nishimoto N. Photoinduced adsorption of oligonucleotides on polyvinyl chloride films containing malachite green derivative. SOFT MATTER 2023; 19:2058-2063. [PMID: 36779852 DOI: 10.1039/d2sm01163h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
DNA adsorption on the micrometer scale in a simple and cost-effective manner has received considerable interest. We prepared a film by casting an organic solvent containing polyvinyl chloride and a malachite green derivative, which can be photoionized to afford a cationic moiety for interaction with DNA. In this article, we report photoinduced oligonucleotide adsorption on a film that offers spatial and temporal control over oligonucleotide adsorption. Fluorescence microscopy was used to observe the oligonucleotide adsorption. Oligonucleotides of various sequences and lengths were also examined. UV irradiation using a photomask having 100 μm-diameter holes promoted the oligonucleotide adsorption on the film, whereas there was hardly any oligonucleotide adsorbed on the non-irradiated area. We found that the nucleobase contributed to the adsorption and part of the anchor in the oligonucleotide chain was responsible for the adsorption on the film.
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Affiliation(s)
- Ryoko M Uda
- Department of Chemical Engineering, National Institute of Technology, Nara college, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
| | - Noriko Nishimoto
- Department of Chemical Engineering, National Institute of Technology, Nara college, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
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2
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Yan S, Peck JM, Ilgu M, Nilsen-Hamilton M, Lamm MH. Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer. ACS OMEGA 2020; 5:20187-20201. [PMID: 32832772 PMCID: PMC7439393 DOI: 10.1021/acsomega.0c01867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six de novo predicted 3D structures. Each of the six de novo predicted structures is energy minimized in solution and equilibrated with MD simulations at high temperature. Ten conformations from these six high-temperature equilibration runs are selected as initial conformations for further simulations at ambient temperature. In total, we conducted 60 independent MD simulations, each with a duration of 100 ns, to study the conformation and dynamics of the aptamer. For each group of 10 independent simulations that originated from a particular de novo predicted structure, we evaluated the potential energy distribution of the RNA and used recurrence quantification analysis to examine the sampling of RNA conformational transitions. To assess the impact of starting from different de novo predicted structures, we computed the density of structure projection on principal components to compare the regions sampled by the different groups of ten independent simulations. The recurrence rate and dependence of initial conformation among the groups were also compared. We stress the necessity of using different initial configurations as simulation starting points by showing long simulations from different initial structures suffer from being trapped in different states. Finally, we summarized the sampling efficiency for the complete set of 60 independent simulations and determined regions of under-sampling on the potential energy landscape. The results suggest that conducting multiple independent simulations using a diverse set of de novo predicted structures is a promising approach to achieve sufficient sampling. This approach avoids undesirable outcomes, such as the problem of the RNA aptamer being trapped in a local minimum. For others wishing to conduct multiple independent simulations, the analysis protocol presented in this study is a guide for examining overall sampling and determining if more simulations are necessary for sufficient sampling.
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Affiliation(s)
- Shuting Yan
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Jason M. Peck
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Muslum Ilgu
- Roy
J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
- Aptalogic
Inc., Ames, Iowa 50014, United States
- Department
of Biological Sciences, Middle East Technical
University, Ankara, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy
J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
- Aptalogic
Inc., Ames, Iowa 50014, United States
| | - Monica H. Lamm
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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3
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Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
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Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
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4
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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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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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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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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10
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Bernard Da Costa J, Dieckmann T. Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer. MOLECULAR BIOSYSTEMS 2011; 7:2156-63. [PMID: 21523267 DOI: 10.1039/c1mb05075c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of small molecule targets by RNA aptamers provides an excellent model to study the versatility of RNA function. The malachite green aptamer binds and recognizes its ligand via stacking and electrostatic interactions. The binding of the aptamer to its original selection target and three related molecules was determined by isothermal titration calorimetry, equilibrium dialysis, and fluorescence titration. The results reveal that the entropy of complex formation plays a large role in determining binding affinity and ligand specificity. These data combined with previous structural studies show that metal ions are required to stabilize the complexes with non-native ligands whereas the complex with the original selection target is stable at low salt and in the absence of divalent metal ions.
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Affiliation(s)
- Jason Bernard Da Costa
- University of Waterloo, Dept. of Chemistry, 200 University Ave West, Waterloo, ON, Canada
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Wang T, Hoy JA, Lamm MH, Nilsen-Hamilton M. Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity. J Am Chem Soc 2010; 131:14747-55. [PMID: 19778045 DOI: 10.1021/ja902719q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as "induced fit". But, it is not known to what extent this structural flexibility affects the integrity of the target-aptamer interaction. Using the malachite green aptamer (MGA) as a model system, we show that the MGA can protect its bound target, malachite green (MG), from oxidation over several days. Protection is reversed by an oligonucleotide complementary to the MGA binding pocket. Computational cavity analysis of the MGA-MG structure predicted that MG oxidation is protected because a molecule as small as an OH(-) is sterically excluded from the C1 position of the bound MG. These results suggest that, while the MGA-MG interface is sufficiently coherent to prevent OH(-) penetration, the bases involved in the interaction are sufficiently mobile that they can exchange out of the MG binding interface to hybridize with a complementary oligonucleotide. The computational predictions were confirmed experimentally using variants of the MGA with single base changes in the binding pocket. This work demonstrates the successful application of molecular dynamics simulations and cavity analysis in determining the effects of sequence variations on the structure of a small single-stranded nucleic acid. It also shows that a nucleic acid aptamer can control access to specific chemical groups on its target, which suggests that aptamers might be applied for selectively protecting small molecules from modification.
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Affiliation(s)
- Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch. J Mol Graph Model 2009; 28:37-45. [PMID: 19380244 DOI: 10.1016/j.jmgm.2009.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 03/18/2009] [Accepted: 03/21/2009] [Indexed: 12/25/2022]
Abstract
Recent experimental study [S.D. Gilbert, S.J. Mediatore, R.T. Batey, Modified pyrimidine specifically bind the purine riboswitch, J. Am. Chem. Soc. 128 (2006) 14214-14215] demonstrated that the purine riboswitch could specifically bind some ligands other than purines such as amino-pyrimidines, and the authors proposed that the five-membered ring of purine was not required for recognition. To get insight into the interaction details, we used molecular docking method to investigate the interactions of a mutant form of guanine riboswitch with a series of amino-purines, amino-pyrimidines and imidazole derivatives, and employed molecular simulation method to study the dynamic behavior of the selected complexes. The calculation results reveal that (1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleobases including U22, U47, U51 and U74, which is consistent with the experimental results, while the two imidazole derivatives adopt other binding modes; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the number and position of amino substituents could seriously affect the binding of pyrimidines. As riboswitches are potentially excellent candidates for antibiotic therapeutics, these findings may be useful for understanding the range of compounds that riboswitch can specifically recognize.
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Fluorinated analogs of malachite green: synthesis and toxicity. Molecules 2008; 13:986-94. [PMID: 18463600 PMCID: PMC6245195 DOI: 10.3390/molecules13040986] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 04/22/2008] [Accepted: 04/22/2008] [Indexed: 11/16/2022] Open
Abstract
A series of fluorinated analogs of malachite green (MG) have been synthesized and their toxicity to Saccharomyces cerevisiae and a human ovarian epithelial cell line examined. The toxicity profiles were found to be different for these two species. Two analogs, one with 2,4-difluoro substitution and the other with 2-fluoro substitution seem to be the most promising analogs because they showed the lowest toxicity to the human cells.
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Bhasikuttan A, Mohanty J, Nau W, Pal H. Efficient Fluorescence Enhancement and Cooperative Binding of an Organic Dye in a Supra-biomolecular Host–Protein Assembly. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604757] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bhasikuttan AC, Mohanty J, Nau WM, Pal H. Efficient Fluorescence Enhancement and Cooperative Binding of an Organic Dye in a Supra-biomolecular Host–Protein Assembly. Angew Chem Int Ed Engl 2007; 46:4120-2. [PMID: 17443829 DOI: 10.1002/anie.200604757] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Roy D, Sunoj RB. Intramolecular nonbonding interactions in organoseleniums: Quantification using a computational thermochemical approach. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Abstract
In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.
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Affiliation(s)
- Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, 2000 East, 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112, USA.
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