1
|
Kankanamalage DVDW, Tran JHT, Beltrami N, Meng K, Zhou X, Pathak P, Isaacs L, Burin AL, Ali MF, Jayawickramarajah J. DNA Strand Displacement Driven by Host-Guest Interactions. J Am Chem Soc 2022; 144:16502-16511. [PMID: 36063395 PMCID: PMC9479067 DOI: 10.1021/jacs.2c05726] [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] [Indexed: 11/29/2022]
Abstract
Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.
Collapse
Affiliation(s)
| | - Jennifer H T Tran
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Noah Beltrami
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Kun Meng
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Mehnaaz F Ali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | | |
Collapse
|
2
|
Nie H, Wei Z, Ni XL, Liu Y. Assembly and Applications of Macrocyclic-Confinement-Derived Supramolecular Organic Luminescent Emissions from Cucurbiturils. Chem Rev 2022; 122:9032-9077. [PMID: 35312308 DOI: 10.1021/acs.chemrev.1c01050] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cucurbit[n]urils (Q[n]s or CB[n]s), as a classical of artificial organic macrocyclic hosts, were found to have excellent advantages in the fabricating of tunable and smart organic luminescent materials in aqueous media and the solid state with high emitting efficiency under the rigid pumpkin-shaped structure-derived macrocyclic-confinement effect in recent years. This review aims to give a systematically up-to-date overview of the Q[n]-based supramolecular organic luminescent emissions from the confined spaces triggered host-guest complexes, including the assembly fashions and the mechanisms of the macrocycle-based luminescent complexes, as well as their applications. Finally, challenges and outlook are provided. Since this class of Q[n]-based supramolecular organic luminescent emissions, which have essentially derived from the cavity-dependent confinement effect and the resulting assembly fashions, emerged only a few years ago, we hope this review will provide valuable information for the further development of macrocycle-based light-emitting materials and other related research fields.
Collapse
Affiliation(s)
- Haigen Nie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine (Ministry of Educational of China), Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan 410081, China
| | - Zhen Wei
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Xin-Long Ni
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine (Ministry of Educational of China), Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan 410081, China.,Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
3
|
Bikaki M, Kuhnert N. "Thermal Peroxidation" of Dietary Pentapeptides Yields N-Terminal 1,2-Dicarbonyls. Front Nutr 2021; 8:663233. [PMID: 34368205 PMCID: PMC8339318 DOI: 10.3389/fnut.2021.663233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
In this contribution we investigate the thermal degradation of dietary-relevant pentapeptides. Most unsaturated lipids degrade by the well-known peroxidation mechanism. Here we show a degradation mechanism of peptides analogous to lipid peroxidation, forming a series of novel degradation products with possible toxicological relevance. At elevated temperatures above 180°C, pentapeptides with an N-terminal phenylalanine moiety react via a debenzylation to form 1,2-dicabonyl compounds, replacing the N-terminal primary amine. We propose a radical-based reaction mechanism that leads via a common peroxoaminal intermediate to two distinct types of reaction products with a terminal α-1,2 diamide or an α-amide-aldehyde functionality.
Collapse
Affiliation(s)
- Maria Bikaki
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Nikolai Kuhnert
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| |
Collapse
|
4
|
Hennig A, Nau WM. Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays. Front Chem 2020; 8:806. [PMID: 33134264 PMCID: PMC7511663 DOI: 10.3389/fchem.2020.00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.
Collapse
Affiliation(s)
- Andreas Hennig
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,Institute of Chemistry of New Materials, School of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| |
Collapse
|
5
|
Jayapaul J, Schröder L. Probing Reversible Guest Binding with Hyperpolarized 129Xe-NMR: Characteristics and Applications for Cucurbit[ n]urils. Molecules 2020; 25:E957. [PMID: 32093412 PMCID: PMC7070628 DOI: 10.3390/molecules25040957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cucurbit[n]urils (CB[n]s) are a family of macrocyclic host molecules that find various applications in drug delivery, molecular switching, and dye displacement assays. The CB[n]s with n = 5-7 have also been studied with 129Xe-NMR. They bind the noble gas with a large range of exchange rates. Starting with insights from conventional direct detection of bound Xe, this review summarizes recent achievements with chemical exchange saturation transfer (CEST) detection of efficiently exchanging Xe in various CB[n]-based supramolecular systems. Unprecedented sensitivity has been reached by combining the CEST method with hyperpolarized Xe, the production of which is also briefly described. Applications such as displacement assays for enzyme activity detection and rotaxanes as emerging types of Xe biosensors are likewise discussed in the context of biomedical applications and pinpoint future directions for translating this field to preclinical studies.
Collapse
Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
| |
Collapse
|
6
|
Beatty MA, Selinger AJ, Li Y, Hof F. Parallel Synthesis and Screening of Supramolecular Chemosensors That Achieve Fluorescent Turn-on Detection of Drugs in Saliva. J Am Chem Soc 2019; 141:16763-16771. [DOI: 10.1021/jacs.9b07073] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Meagan A. Beatty
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - Allison J. Selinger
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - YuQi Li
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| |
Collapse
|
7
|
Nour HF, Lopez-Periago AM, Kuhnert N. Probing the mechanism and dynamic reversibility of trianglimine formation using real-time electrospray ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1070-1080. [PMID: 22467457 DOI: 10.1002/rcm.6203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE The [3+3]-cyclocondensation reactions of chiral (1R,2R)-1,2-diaminocyclohexane with aromatic or aliphatic bis-aldehydes to form trianglimine macrocycles were reported a decade ago and were believed to proceed through a stepwise mechanistic pathway; however, no intermediates were ever isolated or detected and characterized. METHODS We investigated the mechanism of the [3+3]-cyclocondensation reaction using a selection of dialdehyde starting materials using real-time electrospray ionization time-of-flight mass spectrometry. RESULTS We observed up to a maximum of 16 reaction intermediates along the reaction pathway, more than for any other multistep reaction reported. We also probed the dynamic reversibility of trianglimines using selected small dynamic combinatorial libraries and showed that trianglimine formation is indeed fully reversible. CONCLUSIONS This study represents a significant contribution towards understanding the mechanism of trianglimine formation and its potential applicability can be extended to include other cascade reactions.
Collapse
Affiliation(s)
- Hany F Nour
- School of Engineering and Science, Organic and Analytical Chemistry Laboratory, Jacobs University, 28759, Bremen, Germany
| | | | | |
Collapse
|