1
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Ghani L, Kim S, Ehsan M, Lan B, Poulsen IH, Dev C, Katsube S, Byrne B, Guan L, Loland CJ, Liu X, Im W, Chae PS. Melamine-cored glucosides for membrane protein solubilization and stabilization: importance of water-mediated intermolecular hydrogen bonding in detergent performance. Chem Sci 2023; 14:13014-13024. [PMID: 38023530 PMCID: PMC10664503 DOI: 10.1039/d3sc03543c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Membrane proteins play essential roles in a number of biological processes, and their structures are important in elucidating such processes at the molecular level and also for rational drug design and development. Membrane protein structure determination is notoriously challenging compared to that of soluble proteins, due largely to the inherent instability of their structures in non-lipid environments. Micelles formed by conventional detergents have been widely used for membrane protein manipulation, but they are suboptimal for long-term stability of membrane proteins, making downstream characterization difficult. Hence, there is an unmet need for the development of new amphipathic agents with enhanced efficacy for membrane protein stabilization. In this study, we designed and synthesized a set of glucoside amphiphiles with a melamine core, denoted melamine-cored glucosides (MGs). When evaluated with four membrane proteins (two transporters and two G protein-coupled receptors), MG-C11 conferred notably enhanced stability compared to the commonly used detergents, DDM and LMNG. These promising findings are mainly attributed to a unique feature of the MGs, i.e., the ability to form dynamic water-mediated hydrogen-bond networks between detergent molecules, as supported by molecular dynamics simulations. Thus, MG-C11 is the first example of a non-peptide amphiphile capable of forming intermolecular hydrogen bonds within a protein-detergent complex environment. Detergent micelles formed via a hydrogen-bond network could represent the next generation of highly effective membrane-mimetic systems useful for membrane protein structural studies.
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Affiliation(s)
- Lubna Ghani
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study Seoul 024-55 South Korea
| | - Muhammad Ehsan
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
| | - Baoliang Lan
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Ida H Poulsen
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Chandra Dev
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock Texas 79430 USA
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen Copenhagen DK-2200 Denmark
| | - Xiangyu Liu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, and Bioengineering Lehigh University Bethlehem PA 18015 USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University Ansan 155-88 South Korea
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2
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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3
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Schuster GB, Hud NV, Alenaizan A. Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions. J Phys Chem B 2022; 126:10758-10767. [PMID: 36502412 DOI: 10.1021/acs.jpcb.2c05934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
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4
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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5
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Prebiotic synthesis of noncanonical nucleobases under plausible alkaline hydrothermal conditions. Sci Rep 2022; 12:15140. [PMID: 36071125 PMCID: PMC9452575 DOI: 10.1038/s41598-022-19474-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Herein, the potential of alkaline hydrothermal environments for the synthesis of possible ancestral pre-RNA nucleobases using cyanide as a primary source of carbon and nitrogen is described. Water cyanide polymerizations were assisted by microwave radiation to obtain high temperature and a relatively high pressure (MWR, 180 °C, 15 bar) and were also carried out using a conventional thermal system (CTS, 80 °C, 1 bar) to simulate subaerial and aerial hydrothermal conditions, respectively, on the early Earth. For these syntheses, the initial concentration of cyanide and the diffusion effects were studied. In addition, it is well known that hydrolysis conditions are directly related to the amount and diversity of organic molecules released from cyanide polymers. Thus, as a first step, we studied the effect of several hydrolysis procedures, generally used in prebiotic chemistry, on some of the potential pre-RNA nucleobases of interest, together with some of their isomers and/or deamination products, also presumably formed in these complex reactions. The results show that the alkaline hydrothermal scenarios with a relatively constant pH are good geological scenarios for the generation of noncanonical nucleobases using cyanide as a prebiotic precursor.
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Petelski AN, Pamies SC, Márquez MJV, Sosa GL, Peruchena NM. Impact of covalent modifications on the hydrogen bond strengths in diaminotriazine supramolecules. Chemphyschem 2022; 23:e202200151. [PMID: 35420735 DOI: 10.1002/cphc.202200151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/13/2022] [Indexed: 11/10/2022]
Abstract
Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group -NHR, and the replacement of the whole -NH 2 group (R = H, F, CH 3 and COCH 3 ). Through our dispersion-corrected density functional theory computations, we explain which covalent modification will show the best self-assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N-H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group notably boosts the strength of hexameric rosettes. This research, therefore, provides molecular tools for the rational design of emerging materials based on uneven hydrogen-bonded arrangements.
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Affiliation(s)
- Andre Nicolai Petelski
- Universidad Tecnológica Nacional: Universidad Tecnologica Nacional, Chemical Engioneering, French 414, H3500CHJ, Resistencia, ARGENTINA
| | - Silvana Carina Pamies
- Universidad Tecnológica Nacional: Universidad Tecnologica Nacional, Chemical Engineering, French 414, H3500CHJ, Resistencia, ARGENTINA
| | - María Josefina Verónica Márquez
- Universidad Tecnológica Nacional: Universidad Tecnologica Nacional, Chemical Engineering, French 414, H3500CHJ, Resistencia, ARGENTINA
| | - Gladis Laura Sosa
- Universidad Tecnológica Nacional: Universidad Tecnologica Nacional, Chemical Engineering, French 414, H3500CHJ, Resistencia, ARGENTINA
| | - Nélida María Peruchena
- National University of the Northeast: Universidad Nacional del Nordeste, Chemistry, Avenida Libertad 5460, 3400, Corrientes, ARGENTINA
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7
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Wang J, Li H, Yue D. Enhanced adsorption of humic/fulvic acids onto urea-derived graphitic carbon nitride. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127643. [PMID: 34740511 DOI: 10.1016/j.jhazmat.2021.127643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/10/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Since humic substances (HSs) can cause environmental problems, their elimination has been attracting more and more concerns. In this study, we investigated HSs adsorption onto urea-derived graphitic carbon nitride (CNU) and elucidated adsorption mechanisms (i.e. heterogeneity, interface rearrangement, and multiple interactions). The adsorption capacity of CNUs was enhanced as increasing calcination temperature and time. Among CNUs, CNU-575-3 showed the highest adsorption capacity; the maximum adsorption capacities for humic acid (HA) and fulvic acid (FA) were 164.06 mg C/g, 14.61 L/cm·g, 91.12 mg C/g, and 5.34 L/cm·g, respectively. The adsorption affinity of CNUs mainly correlated with the amount of amino groups, and that of HSs components was dependent on aromaticity due to π-π interactions. More specifically, terrestrial humic-like and fulvic-like components within HA and FA showed the greatest adsorption affinity, respectively. HSs adsorption was remarkably affected by pH, alkali metals, and alkali earth metals via electrostatic interactions, H-bonding, cation bridge, and configurational effect. In addition, the adsorption of Elliott soil HA (ESHA) and the landfill leachate concentrate by CNUs was also highly efficient. This study shows the great promise of CNUs for HSs adsorption in waters and wastewaters.
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Affiliation(s)
- Jianchao Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongxin Li
- Beijing University of Civil Engineering and Architecture, School of Environment and Energy Engineering, Beijing 100044, China
| | - Dongbei Yue
- School of Environment, Tsinghua University, Beijing 100084, China.
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8
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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9
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Chattaraj KG, Paul S. Appraising the potency of small molecule inhibitors and their graphene surface-mediated organizational attributes on uric acid-melamine clusters. Phys Chem Chem Phys 2022; 24:1029-1047. [PMID: 34927187 DOI: 10.1039/d1cp03695e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uric acid (UA) and melamine (MM) crystallization in humans is associated with adverse medical conditions, including the germination of kidney stones, because of their low solubility. The growth of kidney stones, usually formed on renal papillary facades, is accomplished on the matrix-coated surface by the aggregation of preformed crystals or secondary crystal nucleation. Therefore, the effects of inhibitors such as theobromine (TB) and allopurinol (AP) on MM-UA aggregation are investigated by employing classical molecular dynamics simulations on a graphene surface. This impersonates the exact essence of the precipitation of kidney stones. The interaction between MM-UA is very intense and, thus, large clusters are formed on the surface. The presence of TB and AP will, however, substantially inhibit their aggregation. TB and AP significantly impede UA aggregation in particular. Therefore, lower order UA clusters are formed. These smaller UA clusters then pull a lower number of MM towards themselves, resulting in a smaller order UA-MM cluster. MM and UA aggregation on a 2D graphene surface is found to be spontaneous. There is no difference in these molecules' adsorption with a change in the force field parameters (i.e., GAFF and OPLS-AA) for graphene. Moreover, the greater the surface area of graphene, the more molecules are absorbed. The solute-surface van der Waals interaction energy plays a driving force in the adsorption of solute molecules on the surface. In addition, interactions like hydrogen bonding and π-stacking over the graphene surface involve binding all like molecules. These aggregated solute molecules strongly attract more like molecules until all solute molecules are adsorbed on the graphene surface, as estimated by enhanced sampling. The molecular origin of graphene exfoliation by MM is also described here. The present work helps to design novel kidney stone inhibitors.
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Affiliation(s)
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India, 781039.
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10
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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11
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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12
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Imoro N, Shilovskikh VV, Nesterov PV, Timralieva AA, Gets D, Nebalueva A, Lavrentev FV, Novikov AS, Kondratyuk ND, Orekhov ND, Skorb EV. Biocompatible pH-Degradable Functional Capsules Based on Melamine Cyanurate Self-Assembly. ACS OMEGA 2021; 6:17267-17275. [PMID: 34278113 PMCID: PMC8280711 DOI: 10.1021/acsomega.1c01124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Development of adaptive self-regulating materials and chemical-biological systems-self-healing, self-regulating, etc.-is an advanced modern trend. The very sensitive pH-controlled functionality of supramolecular assemblies is a very useful tool for chemical and biochemical implementations. However, the assembly process can be tuned by various factors that can be used for both better functionality control and further functionalization such as active species, e.g., drugs and dyes, and encapsulation. Here, the effect of a dye, sodium fluorescein (uranine) (FL), on the formation of a self-assembled melamine cyanurate (M-CA) structure is investigated and calculated with density functional theory (DFT) and molecular dynamics. Interestingly, the dye greatly affects the self-assembly process at early stages from the formation of dimers, trimers, and tetramer to nucleation control. The supramolecular structure disassembly and subsequent release of trapped dye occurred under both high- and low-pH conditions. This system can be used for time-prolonged bacterial staining and development of supramolecular capsules for the system chemistry approach.
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Affiliation(s)
- Nfayem Imoro
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
| | | | - Pavel V. Nesterov
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
| | | | - Dmitry Gets
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
| | - Anna Nebalueva
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
| | - Filipp V. Lavrentev
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
| | | | - Nikolay D. Kondratyuk
- Moscow
Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
- Joint
Institute for High Temperatures of the Russian Academy of Sciences, 13 Izhorskaya Bd 2, Moscow 125412, Russian Federation
| | - Nikita D. Orekhov
- Moscow
Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
- Joint
Institute for High Temperatures of the Russian Academy of Sciences, 13 Izhorskaya Bd 2, Moscow 125412, Russian Federation
- Bauman
Moscow State Technical University, 2nd Baumanskaya Str., 5, Moscow 105005, Russia
| | - Ekaterina V. Skorb
- ITMO
University, Lomonosova str. 9, St. Petersburg 191002, Russian Federation
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13
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Schuster GB, Cafferty BJ, Karunakaran SC, Hud NV. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J Am Chem Soc 2021; 143:9279-9296. [PMID: 34152760 DOI: 10.1021/jacs.0c13081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Brian J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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14
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Meena CL, Singh D, Kizhakeetil B, Prasad M, George M, Tothadi S, Sanjayan GJ. Triazine-Based Janus G-C Nucleobase as a Building Block for Self-Assembly, Peptide Nucleic Acids, and Smart Polymers. J Org Chem 2021; 86:3186-3195. [PMID: 33523657 DOI: 10.1021/acs.joc.0c02530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This communication reports on the utility of a triazine-based self-assembling system, reminiscent of a Janus G-C nucleobase, as a building block for developing (1) supramolecular polymers, (2) peptide nucleic acids (PNAs), and (3) smart polymers. The strategically positioned self-complementary triple H-bonding arrays DDA and AAD facilitate efficient self-assembly, leading to a linear supramolecular polymer.
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Affiliation(s)
- Chhuttan L Meena
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Dharmendra Singh
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Bhavya Kizhakeetil
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Manasa Prasad
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Malini George
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Srinu Tothadi
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
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15
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Alenaizan A, Fauché K, Krishnamurthy R, Sherrill CD. Noncovalent Helicene Structure between Nucleic Acids and Cyanuric Acid. Chemistry 2021; 27:4043-4052. [DOI: 10.1002/chem.202004390] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/08/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
- Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta GA 30332-0400 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Kévin Fauché
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - C. David Sherrill
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
- Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta GA 30332-0400 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0765 USA
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16
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Anderson BA, Fauché K, Karunakaran SC, Yerabolu JR, Hud NV, Krishnamurthy R. The Unexpected Base‐Pairing Behavior of Cyanuric Acid in RNA and Ribose versus Cyanuric Acid Induced Helicene Assembly of Nucleic Acids: Implications for the Pre‐RNA Paradigm. Chemistry 2021; 27:4033-4042. [DOI: 10.1002/chem.202004397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/08/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Brooke A. Anderson
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Kévin Fauché
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Jayasudhan R. Yerabolu
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
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17
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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18
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Kabata Glowacki S, Koszinowski K, Hübner D, Frauendorf H, Vana P, Diederichsen U. Supramolecular Self-Assembly of β 3 -Peptides Mediated by Janus-Type Recognition Units. Chemistry 2020; 26:12145-12149. [PMID: 32621556 PMCID: PMC7539953 DOI: 10.1002/chem.202003107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 01/18/2023]
Abstract
To gain mechanistic insights, natural systems with biochemical relevance are inspiring for the creation of new biomimetics with unique properties and functions. Despite progress in rational design and protein engineering, folding and intramolecular organization of individual components into supramolecular structures remains challenging and requires controlled methods. Foldamers, such as β-peptides, are structurally well defined with rigid conformations and suitable for the specific arrangement of recognition units. Herein, we show the molecular arrangement and aggregation of β3 -peptides into a hexameric helix bundle. For this purpose, β-amino acid side chains were modified with cyanuric acid and triamino-s-triazine as complementary recognition units. The pre-organization of the β3 -peptides leads these Janus molecule pairs into a hexameric arrangement and a defined rosette nanotube by stacking. The helical conformation of the subunits was indicated by circular dichroism spectroscopy, while the supramolecular arrangement was detected by dynamic light scattering and confirmed by high-resolution electrospray ionization mass spectrometry (ESI-HRMS).
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Affiliation(s)
- Selda Kabata Glowacki
- Institute of Organic and Biomolecular ChemistryGeorg-August-University GöttingenTammannstrasse 237077GöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (cfBIN)University Medical Center Göttingenvon-Sieboldstrasse 3a37075GöttingenGermany
| | - Konrad Koszinowski
- Institute of Organic and Biomolecular ChemistryGeorg-August-University GöttingenTammannstrasse 237077GöttingenGermany
| | - Dennis Hübner
- Institute of Physical ChemistryGeorg-August-University GöttingenTammannstrasse 637077GöttingenGermany
| | - Holm Frauendorf
- Institute of Organic and Biomolecular ChemistryGeorg-August-University GöttingenTammannstrasse 237077GöttingenGermany
| | - Philipp Vana
- Institute of Physical ChemistryGeorg-August-University GöttingenTammannstrasse 637077GöttingenGermany
| | - Ulf Diederichsen
- Institute of Organic and Biomolecular ChemistryGeorg-August-University GöttingenTammannstrasse 237077GöttingenGermany
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19
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Liang Y, Miao S, Mao J, DeSantis C, Bong D. Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs. Biochemistry 2020; 59:2410-2418. [PMID: 32519542 DOI: 10.1021/acs.biochem.0c00362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na+) over the parallel topology (K+) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na+) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiqin Miao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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20
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Miao S, Liang Y, Marathe I, Mao J, DeSantis C, Bong D. Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains. J Am Chem Soc 2019; 141:9365-9372. [PMID: 31094510 PMCID: PMC7043357 DOI: 10.1021/jacs.9b03435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine side chain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible. A compact bPNA+binding site of two U6 domains can be genetically encoded to replace existing 6 bp stem elements at virtually any location within an RNA transcript. We thus replaced internal 6 bp RNA stems that supported loop regions with 6 base-triple hybrid stems using fluorophore-labeled bPNA+. As the loop regions engaged in RNA tertiary interactions, the labeled hybrid stems provided a fluorescent readout; bPNA+ enabled this readout without covalent chemical modification or introduction of new structural elements. This strategy was demonstrated to be effective for reporting on widely observed RNA tertiary interactions such as intermolecular RNA-RNA kissing loop dimerization, RNA-protein binding, and intramolecular RNA tetraloop-tetraloop receptor binding, illustrating the potential general utility of this method. The modest 6 bp stem binding footprint of bPNA+ makes the hybrid stem replacement method practical for noncovalent installation of synthetic probes of RNA interactions. We anticipate that bPNA+ structural probes will be useful for the study of tertiary interactions in long noncoding RNAs.
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21
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Liang Y, Mao J, Bong D. Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis. Methods Enzymol 2019; 623:151-175. [PMID: 31239045 DOI: 10.1016/bs.mie.2019.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biochemistry and structural biology of the hammerhead ribozyme (HHR) have been well elucidated. The secondary and tertiary structural elements that enable sugar-phosphate bond scission to be catalyzed by this RNA are clearly understood. We have taken advantage of this knowledge base to test the extent to which synthetic molecules, may be used to trigger structure in secondary structure and tertiary interactions and thereby control HHR catalysis. These molecules belong to a family of molecules we generally call "bPNAs" based on our work on bifacial peptide nucleic acid (bPNA). This family of molecules displays the "bifacial" heterocycle melamine, which acts as a base-triple upon capturing two equivalents of thymine or uracil. Loosely structured internal oligouridylate bulges of 4-20 nucleotides can be restructured as triplex hybrid stems upon binding bPNAs. As such, a duplex stem element can be replaced with a bPNA triplex hybrid stem; similarly, a tertiary loop-stem interaction can be replaced with a loop-bPNA-stem complex. The ability to control RNA structure-function facilitates elucidation of these critical aspects of RNA recognition. In this chapter, we discuss how bPNAs are prepared and applied to study structure-function turn on in the hammerhead ribozyme system.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Jie Mao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.
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22
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Ghosh C, Nandi A, Basu S. Supramolecular self-assembly of triazine-based small molecules: targeting the endoplasmic reticulum in cancer cells. NANOSCALE 2019; 11:3326-3335. [PMID: 30724283 DOI: 10.1039/c8nr08682f] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The endoplasmic reticulum (ER) is one of the most important organelles controlling myriads of cellular functions including protein folding/misfolding/unfolding, calcium ion homeostasis and lipid biosynthesis. Subsequently, due to its functional dysregulation in cancer cells, it has emerged as an interesting target for anti-cancer therapy. However, specific targeting of the ER in cancer cells remains a major challenge due to the lack of ER-selective chemical tools. Furthermore, for performing multiple cellular functions the ER is dependent on the nucleus through complicated cross-talk. Herein, we have engineered a supramolecular self-assembled hexameric rosette structure from two small molecules: tri-substituted triazine and 5-fluorouracil (5-FU). This rosette structure consists of an ER-targeting moiety with a fluorescence tag, an ER-stress inducer and a nuclear DNA damaging drug simultaneously, which further self-assembled into an ER-targeting spherical nano-scale particle (ER-NP). These ER-NPs internalized into HeLa cervical cancer cells by macropinocytosis and specifically localized into the ER to induce ER stress and DNA damage leading to cell death through apoptosis. Interestingly, ER-NPs initiated autophagy, inhibited by a combination of ER-NPs and chloroquine (CQ) to augment cancer cell death. This work has the potential to exploit the concept of supramolecular self-assembly into developing novel nano-scale materials for specific sub-cellular targeting of multiple organelles for future anti-cancer therapy.
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Affiliation(s)
- Chandramouli Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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23
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Petelski AN, Fonseca Guerra C. Designing Self-Assembled Rosettes: Why Ammeline is a Superior Building Block to Melamine. ChemistryOpen 2019; 8:135-142. [PMID: 30740288 PMCID: PMC6356174 DOI: 10.1002/open.201800210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/25/2018] [Indexed: 01/16/2023] Open
Abstract
In supramolecular chemistry, the rational design of self-assembled systems remains a challenge. Herein, hydrogen-bonded rosettes of melamine and ammeline have been theoretically examined by using dispersion-corrected density functional theory (DFT-D). Our bonding analyses, based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA), show that ammeline is a much better building block than melamine for the fabrication of cyclic complexes based on hydrogen bonds. This superior capacity is explained by both stronger hydrogen bonding and the occurrence of a strong synergy.
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Affiliation(s)
- Andre Nicolai Petelski
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Departamento de Ingeniería QuímicaGrupo de Investigación en Química Teórica y Experimental (QuiTEx)Facultad Regional ResistenciaUniversidad Tecnológica NacionalFrench 414H3500CHJResistenciaChacoArgentina
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityThe Netherlands
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24
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Kaur S, Sharma P. Radical pathways for the formation of non-canonical nucleobases in prebiotic environments. RSC Adv 2019; 9:36530-36538. [PMID: 35539032 PMCID: PMC9075218 DOI: 10.1039/c9ra08001e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 11/21/2022] Open
Abstract
Due to the inability of canonical nucleobases (adenine, uracil, guanine and cytosine) to spontaneously form ribonucleosides and base pairs in free form in solution, RNA is believed to be preceded by a primitive information polymer (preRNA). The preRNA is proposed to contain non-canonical, heterocyclic bases that possess the above-mentioned capabilities. An extensive search for such candidate heterocycles has recently revealed that barbituric acid (BA), melamine (MM) and 2,4,6-triaminopyrimidine (TAP) have the capability to spontaneously form ribonucleosides and supramolecular assemblies that are held by Watson–Crick type hydrogen-bonded base pairs involving BA, MM, TAP and cyanuric acid (CA) heterocycles. However, despite this evidence, the prebiotic formation pathways of these heterocycles have not been fully explored. Further, for these heterocycles to interact and assemble into informational polymers under prebiotic conditions, it is expected that they should have formed in the proximity of each other. In this context, the present work employs density functional theory to propose the associated radical based formation pathways starting from cyanamide. Our pathways suggest that cyanamide, its derivatives (malonic acid and urea) and malononitrile can form BA, MM, CA and TAP in the presence of ammonia and hydroxyl radicals. In addition to originating from a common precursor, similarities in the highest reaction barriers (13 to 20 kcal mol−1) obtained for these pathways suggest that these heterocycles may likely form under similar conditions. Specifically, these pathways are relevant to high energy events such as meteoritic impact during the late heavy bombardment period on the early earth, which would have created conditions where radicals might have formed in reasonable concentrations. Overall, the present study emphasizes the importance of cyanamide in prebiotic heterocycle formation. The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.![]()
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
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25
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Chattaraj KG, Paul S. Understanding of Structure and Thermodynamics of Melamine Association in Aqueous Solution from a Unified Theoretical and Experimental Approach. J Chem Inf Model 2018; 58:1610-1624. [PMID: 30040417 DOI: 10.1021/acs.jcim.8b00231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation propensity of melamine molecules in aqueous solutions in a range of melamine concentrations is investigated by means of a combination of theoretical and experimental approaches. It is observed that the hydrogen bonding interactions of sp3 nitrogen atoms of one melamine with sp2 nitrogen atoms of another melamine play a major role in the melamine association. This finding is complemented by the observed favorable electrostatic energies between melamine molecules. The estimation of the orientational probability of melamine aromatic ring rules out any role of π-π interaction in melamine association. Further, the quantum chemical calculations suggest that a melamine molecule prefers to bind with another like molecule with a dihedral angle ranging from 36° to 46°. We have also determined the dimer existence autocorrelation functions to investigate the melamine-dimer stability with time in aqueous solution. Our results are well validated by the experimental findings (Chapman, R. P.; Averell, P. R.; Harris, R. R. Solubility of Melamine in Water. Ind. Eng. Chem. 1943, 35, 137-138. Ahromi, A. J.; Moosheimer, U. Oxygen Barrier Coatings Based on Supramolecular Assembly of Melamine. Macromolecules 2000, 33, 7582-7587. Yang, C.; Liu. Y. Studying on the Steady-State and Time-Resolved Fluorescence Characteristics of Melamine. Spectrochim. Acta A 2010, 75, 1329-1332. Mircescu, N. E.; Oltean, M.; Chis, V.; Leopold, N. FTIR, FT-Raman, SERS and DFT study on Melamine. Vib. Spectrosc. 2012, 62, 165-171. Makowski. S. J.; Lacher. M.; Schnick. W. Supramolecular Hydrogenbonded Structures between Melamine and N-Heterocycles. J. Mol. Struct. 2012, 1013, 19-25. Li, Z.; Chen, G.; Xu, Y.; Wang, X.; Wang, Z. Study of the Structural and Spectral Characteristics of C3N3(NH2)3(n = 1-4) Clusters. J. Phys. Chem. A 2013, 117, 12511-12518. Li, P.; Arman, D. H.; Wang, H.; Weng, L.; Alfooty, K.; Angawi, R. F.; Chen. B. Solvent Dependent Structures of Melamine: Porous or Non-porous. Cryst. Growth Des. 2015, 15, 1871-1875. Chen, J.; Lei, X.; Peng, B. Study on the Fluorescence Spectra of Melamine in Pure Milk. J. Opt. 2017, 46, 183-186.). Moreover, the thermodynamics of melamine association reveals that the association process is essentially driven by enthalpy, and this enthalpy-driven phenomenon is also confirmed by the experimental isothermal titration calorimetry measurements.
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Affiliation(s)
| | - Sandip Paul
- Department of Chemistry , Indian Institute of Technology , Guwahati , Assam , India 781039
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26
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Cantú R, Shoemaker JA, Kelty CA, Wymer LJ, Behymer TD, Dufour AP, Magnuson ML. Integrated preservation and sample clean up procedures for studying water ingestion by recreational swimmers via urinary biomarker determination. Anal Chim Acta 2017; 982:104-111. [PMID: 28734349 DOI: 10.1016/j.aca.2017.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 11/25/2022]
Abstract
The use of cyanuric acid as a biomarker for ingestion of swimming pool water may lead to quantitative knowledge of the volume of water ingested during swimming, contributing to a better understanding of disease resulting from ingestion of environmental contaminants. When swimming pool water containing chlorinated cyanurates is inadvertently ingested, cyanuric acid is excreted quantitatively within 24 h as a urinary biomarker of ingestion. Because the volume of water ingested can be quantitatively estimated by calculation from the concentration of cyanuric acid in 24 h urine samples, a procedure for preservation, cleanup, and analysis of cyanuric acid was developed to meet the logistical demands of large scale studies. From a practical stand point, urine collected from swimmers cannot be analyzed immediately, given requirements of sample collection, shipping, handling, etc. Thus, to maintain quality control to allow confidence in the results, it is necessary to preserve the samples in a manner that ensures as quantitative analysis as possible. The preservation and clean-up of cyanuric acid in urine is complicated because typical approaches often are incompatible with the keto-enol tautomerization of cyanuric acid, interfering with cyanuric acid sample preparation, chromatography, and detection. Therefore, this paper presents a novel integration of sample preservation, clean-up, chromatography, and detection to determine cyanuric acid in 24 h urine samples. Fortification of urine with cyanuric acid (0.3-3.0 mg/L) demonstrated accuracy (86-93% recovery) and high reproducibility (RSD < 7%). Holding time studies in unpreserved urine suggested sufficient cyanuric acid stability for sample collection procedures, while longer holding times suggested instability of the unpreserved urine. Preserved urine exhibited a loss of around 0.5% after 22 days at refrigerated storage conditions of 4 °C.
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Affiliation(s)
- Ricardo Cantú
- US Department of Homeland Security, Customs and Border Protection, Southwest Regional Science Center, Houston, TX, USA
| | - Jody A Shoemaker
- US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Catherine A Kelty
- US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Larry J Wymer
- US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Thomas D Behymer
- US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Alfred P Dufour
- US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Matthew L Magnuson
- US Environmental Protection Agency, Office of Research and Development, National Homeland Security Research Center, 26 W. Martin Luther King Drive, Cincinnati, OH 45268, USA.
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Mao J, DeSantis C, Bong D. Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis. J Am Chem Soc 2017; 139:9815-9818. [PMID: 28691825 DOI: 10.1021/jacs.7b05448] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have identified tris(2-aminoethyl)amine (tren)-derived scaffolds with two (t2M) or four (t4M) melamine rings that can target oligo T/U domains in DNA/RNA. Unstructured T-rich DNAs cooperatively fold with the tren derivatives to form hairpin-like structures. Both t2M and t4M act as functional switches in a family of hammerhead ribozymes deactivated by stem or loop replacement with a U-rich sequence. Catalysis of bond scission in these hammerhead ribozymes could be restored by putative t2M/t4M refolding of stem secondary structure or tertiary bridging interactions between loop and stem. The simplicity of the t2M/t4M binding site enables programming of allostery in RNAs, recoding oligo-U domains as potential sites for secondary structure or tertiary contact. In combination with a facile and general method for installation of the t2M motif on primary amines, the method described herein streamlines design of synthetic allosteric riboswitches and small molecule-nucleic acid complexes.
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Affiliation(s)
- Jie Mao
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Evolution of the hydrogen-bonding motif in the melamine-cyanuric acid co-crystal: a topological study. J Mol Model 2016; 22:202. [PMID: 27491851 DOI: 10.1007/s00894-016-3070-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/10/2016] [Indexed: 11/27/2022]
Abstract
The melamine (M)/cyanuric acid (CA) supramolecular system is perhaps one of the most exploited in the field of self-assembly because of the high complementarity of the components. However, it is necessary to investigate further the factors involved in the assembly process. In this study, we analyzed a set of 13 M n /CA m clusters (with n , m = 1, 2, 3), taken from crystallographic data, to characterize the nature of the hydrogen bonds involved in the self-assembly of these components as well as to provide greater understanding of the phenomenon. The calculations were performed at the B3LYP/6-311++G(d,p) and ω-B97XD (single point) levels of theory, and the interactions were analyzed within the framework of the quantum theory of atoms in molecules and by means of molecular electrostatic potential maps. Our results show that the stablest structure is the rosette-type motif and the aggregation mechanism is governed by a combination of cooperative and anticooperative effects. Our topological results explain the polymorphism in the self-assembly of coadsorbed monolayers of M and CA. Graphical abstract The aggregation steps of the melamine-cyanuric co-crystal is driven by a hydrogen-bonded network which is governed by a complex combination of cooperative and anticooperative effects.
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Avakyan N, Greschner AA, Aldaye F, Serpell CJ, Toader V, Petitjean A, Sleiman HF. Reprogramming the assembly of unmodified DNA with a small molecule. Nat Chem 2016; 8:368-76. [PMID: 27001733 DOI: 10.1038/nchem.2451] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023]
Abstract
The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.
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Affiliation(s)
- Nicole Avakyan
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Andrea A Greschner
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,INRS: Centre Énergie Matériaux Télécommunications, 1650 Boul. Lionel-Boulet, Varennes Quebec J3X 1S2, Canada
| | - Faisal Aldaye
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Christopher J Serpell
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,School of Physical Sciences, Ingram Building, University of Kent, Canterbury CT2 7NH, Kent, UK
| | - Violeta Toader
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Anne Petitjean
- Department of Chemistry, Queen's University, Chernoff Hall, 90 Bader Lane, Kingston Ontario K7L 3N6, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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30
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Shibata M, Satoh K, Ehara S. Thermosetting bismaleimide resins generating covalent and multiple hydrogen bonds. J Appl Polym Sci 2015. [DOI: 10.1002/app.43121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mitsuhiro Shibata
- Department of Life and Environmental Sciences, Faculty of Engineering; Chiba Institute of Technology; 2-17-1, Tsudanuma Narashino Chiba 275-0016 Japan
| | - Kazuki Satoh
- Department of Life and Environmental Sciences, Faculty of Engineering; Chiba Institute of Technology; 2-17-1, Tsudanuma Narashino Chiba 275-0016 Japan
| | - Shouta Ehara
- Department of Life and Environmental Sciences, Faculty of Engineering; Chiba Institute of Technology; 2-17-1, Tsudanuma Narashino Chiba 275-0016 Japan
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31
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Zhou Z, Xia X, Bong D. Synthetic Polymer Hybridization with DNA and RNA Directs Nanoparticle Loading, Silencing Delivery, and Aptamer Function. J Am Chem Soc 2015; 137:8920-3. [PMID: 26138550 DOI: 10.1021/jacs.5b05481] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein discrete triplex hybridization of DNA and RNA with polyacrylates. Length-monodisperse triazine-derivatized polymers were prepared on gram-scale by reversible addition-fragmentation chain-transfer polymerization. Despite stereoregio backbone heterogeneity, the triazine polymers bind T/U-rich DNA or RNA with nanomolar affinity upon mixing in a 1:1 ratio, as judged by thermal melts, circular dichroism, gel-shift assays, and fluorescence quenching. We call these polyacrylates "bifacial polymer nucleic acids" (bPoNAs). Nucleic acid hybridization with bPoNA enables DNA loading onto polymer nanoparticles, siRNA silencing delivery, and can further serve as an allosteric trigger of RNA aptamer function. Thus, bPoNAs can serve as tools for both non-covalent bioconjugation and structure-function nucleation. It is anticipated that bPoNAs will have utility in both bio- and nanotechnology.
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Affiliation(s)
- Zhun Zhou
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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32
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Piao X, Xia X, Mao J, Bong D. Peptide Ligation and RNA Cleavage via an Abiotic Template Interface. J Am Chem Soc 2015; 137:3751-4. [PMID: 25747470 DOI: 10.1021/jacs.5b00236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xijun Piao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Xin Xia
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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35
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Colorimetric and visual read-out determination of cyanuric acid exploiting the interaction between melamine and silver nanoparticles. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1163-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Xia X, Piao X, Bong D. Bifacial PNA complexation inhibits enzymatic access to DNA and RNA. Chembiochem 2014; 15:31-6. [PMID: 24259287 PMCID: PMC3896088 DOI: 10.1002/cbic.201300536] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 02/02/2023]
Abstract
FULL STOP: Herein we report the effective in vitro inhibition of transcription, reverse-transcription and exonuclease function by formation of synthetic bPNA-nucleic acid triplex structures. Selective bPNA targeting of both DNA and RNA substrates suggests possible application of bPNAs as synthetic regulators of nucleic acid function.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Xijun Piao
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
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37
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Cafferty BJ, Avirah RR, Schuster GB, Hud NV. Ultra-sensitive pH control of supramolecular polymers and hydrogels: pKa matching of biomimetic monomers. Chem Sci 2014. [DOI: 10.1039/c4sc02182g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
pKa-matched monomers self-assemble into supramolecular polymers at pH 7, producing hydrogels with high pH sensitivity.
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Affiliation(s)
- B. J. Cafferty
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - R. R. Avirah
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - G. B. Schuster
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - N. V. Hud
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
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Abstract
Lipid membrane fusion is a fundamental noncovalent transformation as well as a central process in biology. The complex and highly controlled biological machinery of fusion has been the subject of intense investigation. In contrast, fewer synthetic approaches that demonstrate selective membrane fusion have been developed. Artificial recapitulation of membrane fusion is an informative pursuit in that fundamental biophysical concepts of biomembrane merger may be generally tested in a controlled reductionist system. A key concept that has emerged from extensive studies on lipid biophysics and biological membrane fusion is that selective membrane fusion derives from the coupling of surface recognition with local membrane disruption, or strain. These observations from native systems have guided the development of de novo-designed biomimetic membrane fusion systems that have unequivocally established the generality of these concepts in noncovalent chemistry. In this Account, we discuss the function and limitations of the artificial membrane fusion systems that have been constructed to date and the insights gained from their study by our group and others. Overall, the synthetic systems are highly reductionist and chemically selective, though there remain aspects of membrane fusion that are not sufficiently understood to permit designed function. In particular, membrane fusion with efficient retention of vesicular contents within the membrane-bound compartments remains a challenge. We discuss examples in which lipid mixing and some degree of vesicle-contents mixing is achieved, but the determinants of aqueous-compartment mixing remain unclear and therefore are difficult to generally implement. The ability to fully design membrane fusogenic function requires a deeper understanding of the biophysical underpinnings of membrane fusion, which has not yet been achieved. Thus, it is critical that biological and synthetic studies continue to further elucidate this biologically important process. Examination of lipid membrane fusion from a synthetic perspective can also reveal the governing noncovalent principles that drive chemically determined release and controlled mixing within nanometer-scale compartments. These are processes that figure prominently in numerous biotechnological and chemical applications. A rough guide to the construction of a functional membrane fusion system may already be assembled from the existing studies: surface-directed membrane apposition may generally be elaborated into selective fusion by coupling to a membrane-disruptive element, as observed over a range of systems that include small-molecule, DNA, or peptide fusogens. Membrane disruption may take different forms, and we briefly describe our investigation of the sequence determinants of fusion and lysis in membrane-active viral fusion peptide variants. These findings set the stage for further investigation of the critical elements that enable efficient, fully functional fusion of both membrane and aqueous compartments and the application of these principles to unite synthetic and biological membranes in a directed fashion. Controlled fusion of artificial and living membranes remains a chemical challenge that is biomimetic of native chemical transport and has a direct impact on drug delivery approaches.
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Affiliation(s)
- Mingming Ma
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Chen MC, Cafferty BJ, Mamajanov I, Gállego I, Khanam J, Krishnamurthy R, Hud NV. Spontaneous prebiotic formation of a β-ribofuranoside that self-assembles with a complementary heterocycle. J Am Chem Soc 2013; 136:5640-6. [PMID: 24328232 DOI: 10.1021/ja410124v] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RNA World hypothesis is central to many current theories regarding the origin and early evolution of life. However, the formation of RNA by plausible prebiotic reactions remains problematic. Formidable challenges include glycosidic bond formation between ribose and the canonical nucleobases, as well as the inability of nucleosides to mutually select their pairing partners from a complex mixture of other molecules prior to polymerization. Here we report a one-pot model prebiotic reaction between a pyrimidine nucleobase (2,4,6-triaminopyrimidine, TAP) and ribose, which produces TAP-ribose conjugates in high yield (60-90%). When cyanuric acid (CA), a plausible ancestral nucleobase, is mixed with a crude TAP+ribose reaction mixture, micrometer-length supramolecular, noncovalent assemblies are formed. A major product of the TAP+ribose reaction is a β-ribofuranoside of TAP, which we term TARC. This nucleoside is also shown to efficiently form supramolecular assemblies in water by pairing and stacking with CA. These results provide a proof-of-concept system demonstrating that several challenges associated with the prebiotic emergence of RNA, or pre-RNA polymers, may not be as problematic as widely believed.
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Affiliation(s)
- Michael C Chen
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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40
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Beecham MP, Clarkson GJ, Hall G, Marsh A. Nanostructures from self-assembling triazine tertiary amine N-oxide amphiphiles. Chemphyschem 2013; 14:3909-15. [PMID: 24203796 DOI: 10.1002/cphc.201300775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Indexed: 11/08/2022]
Abstract
A new set of amphiphilic tertiary amine N-oxides has been prepared and their self-assembly properties observed in aqueous solution by tensiometry, dynamic and static light scattering. X-ray crystallographic analysis of parent amines and sulfoxide congeners indicates the formation of hydrogen-bonded dimers as the primary assembly unit for formation of vesicles in preference to the compact micelles typical of lauryl dimethylamine N-oxide (LDAO). 6-Benzyloxy-N,N'-bis(5-diethylaminopentylamine oxide)[1,3,5]triazine-2,4-diamine forms a 1 μm vesicle observed to entrap fluorescein. The [1,3,5]triazine core thus allows variation of the new self-assembled structures from nano- to micrometre length scales.
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Affiliation(s)
- Matthew P Beecham
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL (UK), Fax: (+44) 24 7652 4112
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41
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Piao X, Xia X, Bong D. Bifacial peptide nucleic acid directs cooperative folding and assembly of binary, ternary, and quaternary DNA complexes. Biochemistry 2013; 52:6313-23. [PMID: 23964711 DOI: 10.1021/bi4008963] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein the structuring of single-stranded thymine-rich DNA sequences into peptide-DNA hairpin triplex structures via designed melamine-thymine nucleobase recognition. Melamine-displaying α-peptides were synthesized with the general form (EM*)n, where M* denotes a lysine residue side chain derivatized with melamine, a bifacial hydrogen bond complement for thymine. We have found that (EM*)n peptides, which we term bifacial peptide nucleic acid (bPNA), function as a noncovalent template for thymine-rich DNA tracts. Unstructured DNA of the general form dTnCmTn are bound to (EM*)n peptides and fold into cooperatively melting 1:1 bPNA-DNA hairpin complexes with dissociation constants in the submicromolar to low nanomolar range for n = 4-10. As the length of the interface (n) is decreased, the melting temperature of the bPNA-DNA complex drops significantly, though Kd increases are less substantial, suggestive of strong enthalpy-entropy compensation. This is borne out by differential scanning calorimetry analysis, which indicates enthalpically driven bPNA-DNA base-stacking that becomes markedly less exothermic as the recognition surface n decreases in size. The recognition interface tolerates a high number of "mismatches" and indicates half-site, or monofacial, recognition between melamine and thymine may occur if only 1 complementary nucleobase is available. Association correlates directly with fractional thymine content, with optimal binding when the number of T-T sites match the number of melamine units. Interestingly, when a DNA host has more T-T sites than melamine sites on bPNA, two or three bPNAs can bind to a single DNA, resulting in ternary and quaternary complexes that have higher thermal stability than the binary (1:1) bPNA-DNA complex, suggestive of cooperative multisite binding. In contrast, when two bPNAs of different lengths bind to the same DNA host, a ternary complex is formed with two melting transitions, corresponding to independent melting of each bPNA component from the complex. These data demonstrate that melamine-displaying bPNA recognize thymine-rich DNA in predictable and multifaceted ways that allow binding affinity, structure stability, and stoichiometry to be tuned through simple bPNA length modification and matching with DNA length. Synthetic bPNA structuring elements may be useful tools for biotechnology.
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Affiliation(s)
- Xijun Piao
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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42
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Cafferty BJ, Gállego I, Chen MC, Farley KI, Eritja R, Hud NV. Efficient Self-Assembly in Water of Long Noncovalent Polymers by Nucleobase Analogues. J Am Chem Soc 2013; 135:2447-50. [DOI: 10.1021/ja312155v] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Brian J. Cafferty
- Department
of Chemistry and
Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - Isaac Gállego
- Department
of Chemistry and
Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - Michael C. Chen
- Department
of Chemistry and
Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - Katherine I. Farley
- Department
of Chemistry and
Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - Ramon Eritja
- Institute for Research in Biomedicine, Parc Científic de Barcelona,
Barcelona 08028, Spain
| | - Nicholas V. Hud
- Department
of Chemistry and
Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
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Lee J, Ahn H, Choi I, Boese M, Park MJ. Enhanced Charge Transport in Enzyme-Wired Organometallic Block Copolymers for Bioenergy and Biosensors. Macromolecules 2012. [DOI: 10.1021/ma300155u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Markus Boese
- National Center for Electron Microscopy, Lawrence Berkeley National
Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
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Zeng Y, Pratumyot Y, Piao X, Bong D. Discrete Assembly of Synthetic Peptide–DNA Triplex Structures from Polyvalent Melamine–Thymine Bifacial Recognition. J Am Chem Soc 2011; 134:832-5. [PMID: 22201288 DOI: 10.1021/ja2099326] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yingying Zeng
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Yaowalak Pratumyot
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Xijun Piao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Dennis Bong
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
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45
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Ma M, Bong D. Protein assembly directed by synthetic molecular recognition motifs. Org Biomol Chem 2011; 9:7296-9. [PMID: 21912803 DOI: 10.1039/c1ob05998j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Tris-functionalized cyanuric acid (TCA) and melamine (TM) selectively recognize each other in aqueous solution with 1 : 1 stoichiometry. We have coupled biotin to TCA and TM to allow pseudo-tetrahedral display of TCA and TM on streptavidin through biotin-ligand binding. Synthetic cyanuric acid/melamine recognition is found to drive selective protein-protein assembly.
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Affiliation(s)
- Mingming Ma
- Department of Chemistry, The Ohio State University, Columbus, USA
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