1
|
Wang F, Bao C, Cui S, Fan J, Zhang Z, Yang W, Yu Y, Li Y. DNA-Templated Click Ligation Chain Reaction Catalyzed by Heterogeneous Cu 2O for Enzyme-Free Amplification and Ultrasensitive Detection of Nucleic Acids. Anal Chem 2024; 96:10028-10037. [PMID: 38853671 DOI: 10.1021/acs.analchem.4c01663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Nucleic acids play a pivotal role in the diagnosis of diseases. However, rapid, cost-efficient, and ultrasensitive identification of nucleic acid targets still represents a significant challenge. Herein, we describe an enzyme-free DNA amplification method capable of achieving accurate and ultrasensitive nucleic acid detection via DNA-templated click ligation chain reaction (DT-CLCR) catalyzed by a heterogeneous nanocatalyst made of Cu2O (hnCu2O). This hnCu2O-DT-CLCR method is built on two cross-amplifying hnCu2O-catalyzed DNA-templated azide-alkyne cycloaddition-driven DNA ligation reactions that boast a fast reaction rate and a high DNA ligation yield in minutes, enabling rapid exponential amplification of specific DNA targets. This newly developed hnCu2O-DT-CLCR-enabled DNA amplification strategy is further integrated with two signal reporting mechanisms to achieve low-cost and easy-to-use biosensors: an electrochemical sensor through the conjugation of a methylene blue redox reporter to a DNA probe used in hnCu2O-DT-CLCR and a colorimetric sensor through the incorporation of the split-to-intact G-quadruplex DNAzyme encoded into hnCu2O-DT-CLCR. Both sensors are able to achieve specific detection of the intended DNA target with a limit of detection at aM ranges, even when challenged in complex biological matrices. The combined hnCu2O-DT-CLCR and sensing strategies offer attractive universal platforms for enzyme-free and yet efficient detection of specific nucleic acid targets.
Collapse
Affiliation(s)
- Fan Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Chenglong Bao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Susu Cui
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Jinlong Fan
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Weiwei Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Yongsheng Yu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, P. R. China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| |
Collapse
|
2
|
Peng Y, Su Z, Jin M, Zhu L, Guan ZJ, Fang Y. Recent advances in porous molecular cages for photocatalytic organic conversions. Dalton Trans 2023; 52:15216-15232. [PMID: 37492891 DOI: 10.1039/d3dt01679j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Photocatalytic organic conversion is considered an efficient, environmentally friendly, and energy-saving strategy for organic synthesis. In recent decades, the molecular cage has emerged as a creative functional material with broad applications in host-guest recognition, drug delivery, catalysis, intelligent materials and other fields. Based on the unique properties of porous molecular cage materials, they provide an ideal platform for leveraging pre-structuring in catalytic reactions and show great potential in various photocatalytic organic reactions. As a result, they have emerged as promising alternatives to conventional molecules or inorganic photocatalysts in redox processes. In this Review, the synthesis strategies based on coordination cages and organic cages, as well as their recent progress in photocatalytic organic conversion, are comprehensively summarized. Finally, we deliver the persistent challenges associated with porous molecular cage compounds that need to be overcome for further development in this field.
Collapse
Affiliation(s)
- Yaoyao Peng
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Zhifang Su
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Meng Jin
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Lei Zhu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Zong-Jie Guan
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Yu Fang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| |
Collapse
|
3
|
Altrichter Y, Bou-Dib P, Kuznia C, Seitz O. Towards a templated reaction that translates RNA in cells into a proaptotic peptide-PNA conjugate. J Pept Sci 2023:e3477. [PMID: 36606596 DOI: 10.1002/psc.3477] [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: 10/13/2022] [Revised: 12/09/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
Nucleic acid-templated chemistry opens the intriguing prospect of triggering the synthesis of drugs only in diseased cells. Herein, we explore the feasibility of using RNA-templated chemical reactions for the activation of a known Smac peptidomimetic compound (SMC), which has proapoptotic activity. Two peptide nucleic acid (PNA) conjugates were used to enable conditional activation of a masked SMC by reduction of an azide either by Staudinger reduction or catalytic photoreduction using a ruthenium complex. The latter provided ~135 nM SMC-PNA on as little as 10 nM (0.01 eq.) template. For the evaluation of the templated azido-SMC reduction system in cellulo, a stable HEK 293 cell line was generated, which overexpressed a truncated, non-functional form of the XIAP mRNA target. We furthermore describe the development of electroporation protocols that enable a robust delivery of PNA conjugates into HEK 293 cells. The action of the reactive PNA conjugates was evaluated by viability and flow cytometric apoptosis assays. In addition, electroporated probes were re-isolated and analyzed by ultra-high performance liquid chromatography (UPLC). Unfortunately, the ruthenium-PNA conjugate proved phototoxic, and treatment of cells with PNA-linked reducing agent and the azido-masked SMC conjugate did not result in a greater viability loss than treatment with scrambled sequence controls. Intracellular product formation was not detectable. A control experiment in total cellular RNA isolate indicated that the templated reaction can in principle proceed in a complex system. The results of this first-of-its-kind study reveal the numerous hurdles that must be overcome if RNA molecules are to trigger the synthesis of pro-apoptotic drugs inside cells.
Collapse
Affiliation(s)
- Yannic Altrichter
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
| | - Peter Bou-Dib
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
| | - Christina Kuznia
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University Berlin, Berlin, Germany
| |
Collapse
|
4
|
Chang LH, Seitz O. RNA-templated chemical synthesis of proapoptotic L- and d-peptides. Bioorg Med Chem 2022; 66:116786. [PMID: 35594647 DOI: 10.1016/j.bmc.2022.116786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/27/2022] [Indexed: 11/02/2022]
Abstract
Nucleic acid-programmed reactions find application in drug screening and nucleic acid diagnosis, and offer prospects for a RNA-sensitive prodrug approach. We aim for the development of a nucleic acid-templated reaction providing nucleic acid-linked molecules that can act on intracellular protein targets. Such reactions would be useful for in situ drug synthesis and activity-based DNA-encoded library screening. In this report, we show native chemical ligation-like chemical peptidyl transfer reactions between peptide-PNA conjugates. The reaction proceeds on RNA templates. As a chemical alternative to ribosomal peptide synthesis access to both L- and d-peptides is provided. In reactions affording 9 to 14 amino acid long pro-apoptotic L- and d-peptides, we found that certain PNA sequence motifs and combinations of cell penetrating peptides (CPPs) cause surprisingly high reactivity in absence of a template. Viability measurements demonstrate that the products of templated peptidyl transfer act on HeLa cells and HEK293 cells. Of note, the presence of cysteine, which is required for NCL chemistry, can enhance the bioactivity. The study provides guidelines for the application of peptide-PNA conjugates in templated synthesis and is of interest for in situ drug synthesis and activity-based DNA-encoded library screening.
Collapse
Affiliation(s)
- Li-Hao Chang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany.
| |
Collapse
|
5
|
Gluhacevic von Krüchten D, Roth M, Seitz O. DNA-Templated Reactions with High Catalytic Efficiency Achieved by a Loss-of-Affinity Principle. J Am Chem Soc 2022; 144:10700-10704. [PMID: 35696276 DOI: 10.1021/jacs.2c03188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic-acid-templated chemical reactions are currently explored for applications in DNA-encoded drug discovery, nucleic acid diagnostics, and theranostics. Of particular interest are reactions enabling the template to gain catalytic activity, so that enzymatic amplification of low copy targets would no longer be necessary. Herein, we introduce a new reaction design relying on the template-controlled cleavage of PNA-spermine conjugates. With turnover frequencies in the range of 3-10 min-1 and a kcat/KM = 1.3 × 106 M-1 s-1, the loss of affinity upon reaction provides a catalytic efficiency equal to most enzymatic conversions and superior to nucleic-acid-templated reactions reported to date.
Collapse
Affiliation(s)
| | - Magdalena Roth
- Department of Chemistry, Humboldt University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| |
Collapse
|
6
|
Houska R, Stutz MB, Seitz O. Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation. Chem Sci 2021; 12:13450-13457. [PMID: 34777764 PMCID: PMC8528049 DOI: 10.1039/d1sc00513h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL). The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.![]()
Collapse
Affiliation(s)
- Richard Houska
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marvin Björn Stutz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| |
Collapse
|
7
|
Roth M, Seitz O. A Self-immolative Molecular Beacon for Amplified Nucleic Acid Detection*. Chemistry 2021; 27:14189-14194. [PMID: 34516006 PMCID: PMC8597011 DOI: 10.1002/chem.202102600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Indexed: 01/18/2023]
Abstract
Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule activates the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self‐immolative molecular beacon (iMB) that escapes the one‐target/one‐probe paradigm. The iMB probe includes a photoreductively cleavable N‐alkyl‐picolinium (NAP) linkage within the loop region. A fluorophore at the 5’‐end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP‐linker cleavage reaction. In the absence of target, the iMB adopts a hairpin shape. Quencher groups prevent photo‐induced cleavage. The iMB opens upon hybridization with a target, and both fluorescent emission as well as photo‐reductive cleavage of the NAP linker can occur. In contrast to previous chemical amplification reactions, iMBs are unimolecular probes that undergo cleavage leading to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pm RNA target within 100 min.
Collapse
Affiliation(s)
- Magdalena Roth
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| |
Collapse
|
8
|
Altrichter Y, Schöller J, Seitz O. Toward conditional control of Smac mimetic activity by RNA-templated reduction of azidopeptides on PNA or 2'-OMe-RNA. Biopolymers 2021; 112:e23466. [PMID: 34287823 DOI: 10.1002/bip.23466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Oligonucleotide templated reactions can be used to control the activity of functional molecules based on the presence of a specific trigger sequence. We report an RNA-controlled reaction system to conditionally restore the N-terminal amino group and thus binding affinity of azide-modified Smac mimetic compounds (SMCs) for their target protein X-linked Inhibitor of Apoptosis Protein (XIAP). Two templated reactions were compared: Staudinger reduction with phosphines and a photocatalytic reaction with Ru(bpy)2 (mcbpy). The latter proved faster and more efficient, especially for the activation of a bivalent SMC, which requires two consecutive reduction steps. The templated reaction proceeds with turnover when 2'-OMe-RNA probes are used, but is significantly more efficient with PNA, catalyzing a reaction in the presence of low, substoichiometric amounts (1%-3%, 10 nM) of target RNA.
Collapse
Affiliation(s)
- Yannic Altrichter
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Justus Schöller
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
9
|
Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
Collapse
Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| |
Collapse
|
10
|
Zavoiura O, Resch-Genger U, Seitz O. Reactive Quantum Dot-Based FRET Systems for Target-Catalyzed Detection of RNA. Methods Mol Biol 2021; 2105:187-198. [PMID: 32088871 DOI: 10.1007/978-1-0716-0243-0_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotide-templated reactions (OTRs) between two reactive hybridization probes allow for the detection of a DNA or RNA of interest by exploiting the target molecule as a catalyst of chemical reactions. The product of such a reaction commonly exhibits distinct fluorescence properties and can be detected by the means of fluorescence spectroscopy. The vast majority of OTR systems utilize organic dyes as fluorescent reporters. However, the use of brighter emitters, such as semiconductor quantum dots (QDs), has potential to improve the sensitivity of detection by providing brighter signals and permitting the use of probes at very low concentrations. Here we report an RNA-templated reaction between two fluorescently labeled peptide nucleic acid (PNA)-based probes, which proceeds on the surface of a QD. The QD-bound PNA probe bears a cysteine functionality, while the other PNA is functionalized with an organic dye as a thioester. OTR between these probes proceeds through a transfer of the organic dye to the QD and can be conveniently monitored via fluorescence resonance energy transfer (FRET) from the QD to the Cy5. The reaction was performed in a conventional fluorescence microplate reader and permits the detection of RNA in the picomolar range.
Collapse
Affiliation(s)
- Oleksandr Zavoiura
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.,Department of Chemistry, Humboldt University of Berlin, Berlin, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, Berlin, Germany.
| |
Collapse
|
11
|
Tom N. Grossmann. Angew Chem Int Ed Engl 2020; 59:20274. [DOI: 10.1002/anie.202005712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
12
|
Tom N. Grossmann. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
13
|
Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
Collapse
Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| |
Collapse
|
14
|
Li J, Quan K, Yang Y, Yang X, Meng X, Huang J, Wang K. Engineering DNAzyme cascade for signal transduction and amplification. Analyst 2020; 145:1925-1932. [PMID: 31989119 DOI: 10.1039/c9an02003a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inspired by the natural enzyme cascade reaction, a multiple DNAzyme cascade platform is engineered to imitate the intracellular process of signal transduction and signal amplification. In this design, when particular stimuli appear, an activated upstream DNAzyme will cleave a well-designed intermediary S1, releasing a downstream DNAzyme that can cleave the reporter substrate S2 to output signals. Thus, the signal is passed from the upstream DNAzyme to the downstream DNAzyme through a well-designed intermediary, accomplishing signal transduction and signal amplification. According to the experimental results, the DNAzyme cascades are capable of improving sensitivity for bioassays compared with that for single DNAzyme-based biocatalysis, which holds promise for potential applications, such as biomolecular computing, logic circuits and precision medicine.
Collapse
Affiliation(s)
- Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Ke Quan
- School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha, P. R. China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Xiangxian Meng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| |
Collapse
|
15
|
Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
Collapse
Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
16
|
Saarbach J, Sabale PM, Winssinger N. Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics. Curr Opin Chem Biol 2019; 52:112-124. [PMID: 31541865 DOI: 10.1016/j.cbpa.2019.06.006] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/07/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas.
Collapse
Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M Sabale
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
| |
Collapse
|
17
|
Seitz O. Templated chemistry for bioorganic synthesis and chemical biology. J Pept Sci 2019; 25:e3198. [PMID: 31309674 PMCID: PMC6771651 DOI: 10.1002/psc.3198] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/24/2022]
Abstract
In light of the 2018 Max Bergmann Medal, this review discusses advancements on chemical biology-driven templated chemistry developed in the author's laboratories. The focused review introduces the template categories applied to orient functional units such as functional groups, chromophores, biomolecules, or ligands in space. Unimolecular templates applied in protein synthesis facilitate fragment coupling of unprotected peptides. Templating via bimolecular assemblies provides control over proximity relationships between functional units of two molecules. As an instructive example, the coiled coil peptide-templated labelling of receptor proteins on live cells will be shown. Termolecular assemblies provide the opportunity to put the proximity of functional units on two (bio)molecules under the control of a third party molecule. This allows the design of conditional bimolecular reactions. A notable example is DNA/RNA-triggered peptide synthesis. The last section shows how termolecular and multimolecular assemblies can be used to better characterize and understand multivalent protein-ligand interactions.
Collapse
Affiliation(s)
- Oliver Seitz
- Department of ChemistryHumboldt University BerlinBerlinGermany
| |
Collapse
|
18
|
RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
Collapse
|
19
|
Abstract
Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.
Collapse
Affiliation(s)
- Alberto Osuna Gálvez
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| |
Collapse
|
20
|
Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| |
Collapse
|
21
|
Zavoiura O, Resch-Genger U, Seitz O. Quantum Dot-PNA Conjugates for Target-Catalyzed RNA Detection. Bioconjug Chem 2018; 29:1690-1702. [PMID: 29694033 DOI: 10.1021/acs.bioconjchem.8b00157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detection of pathogenic nucleic acids remains one of the most reliable approaches for the diagnosis of a broad range of diseases. Current PCR-based methods require experienced personnel and cannot be easily used for point-of-care diagnostics, making alternative strategies for the sensitive, reliable, and cost-efficient detection of pathogenic nucleic acids highly desirable. Here, we report an enzyme-free method for the fluorometric detection of RNA that relies on a target-induced fluorophore transfer onto a semiconductor quantum dot (QD), uses PNA probes as selective recognition elements and can be read out with simple and inexpensive equipment. For QD-PNA conjugates with optimized PNA content, limits of detection of dengue RNA in the range of 10 pM to 100 nM can be realized within 5 h in the presence of a high excess of noncomplementary RNA.
Collapse
Affiliation(s)
- Oleksandr Zavoiura
- Division Biophotonics , Federal Institute for Materials Research and Testing (BAM) , Richard-Willstaetter Strasse 11 , 12489 , Berlin , Germany.,Department of Chemistry , Humboldt University of Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany.,School of Analytical Sciences Adlershof , Humboldt University of Berlin , Unter den Linden 6 , 10099 , Berlin , Germany
| | - Ute Resch-Genger
- Division Biophotonics , Federal Institute for Materials Research and Testing (BAM) , Richard-Willstaetter Strasse 11 , 12489 , Berlin , Germany
| | - Oliver Seitz
- Department of Chemistry , Humboldt University of Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| |
Collapse
|
22
|
Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
Collapse
Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| |
Collapse
|
23
|
Abstract
Probes that detect specific biological materials are indispensable tools for deepening our understanding of various cellular phenomena. In live cell imaging, the probe must emit fluorescence only when a specific substance is detected. In this paper, we introduce a new probe we developed for live cell imaging. Glutathione S-transferase (GST) activity is higher in tumor cells than in normal cells and is involved in the development of resistance to various anticancer drugs. We previously reported the development of a general strategy for the synthesis of probes for detection of GST enzymes, including fluorogenic, bioluminogenic, and 19F-NMR probes. Arylsulfonyl groups were used as caging groups during probe design. The fluorogenic probes were successfully used to quantitate very low levels of GST activity in cell extracts and were also successfully applied to the imaging of microsomal MGST1 activity in living cells. The bioluminogenic and 19F-NMR probes were able to detect GST activity in Escherichia coli cells. Oligonucleotide-templated reactions are powerful tools for nucleic acid sensing. This strategy exploits the target strand as a template for two functionalized probes and provides a simple molecular mechanism for multiple turnover reactions. We developed a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe completed its reaction within 30 s of initiation and amplified the fluorescence signal from 0.5 pM target oligonucleotide by 1500 fold under isothermal conditions. Additionally, we applied the oligonucleotide-templated reaction for molecular releasing and peptide detection.
Collapse
|
24
|
He D, Wong KW, Dong Z, Li HW. Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials. J Mater Chem B 2018; 6:7773-7793. [DOI: 10.1039/c8tb02285b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.
Collapse
Affiliation(s)
- Dinggeng He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
- State Key Laboratory of Developmental Biology of Freshwater Fish
| | - Ka-Wang Wong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Zhenzhen Dong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Hung-Wing Li
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| |
Collapse
|
25
|
Chang D, Kim KT, Lindberg E, Winssinger N. Accelerating Turnover Frequency in Nucleic Acid Templated Reactions. Bioconjug Chem 2017; 29:158-163. [PMID: 29178795 DOI: 10.1021/acs.bioconjchem.7b00663] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acid templated reactions have attracted attention as an important technology to sense oligonucleotides and to translate nucleic acid-based instructions into diverse outputs. Great progress has been made in accelerating the reaction in order to improve signal amplification, reaching rates where substrate turnover rather than chemical reaction is rate limiting. Herein we explore the utility of architectures inspired by three-way junction that yield a cleavage of a strand thus accelerating substrate turnover. We demonstrate that such design can overcome product inhibition in templated reactions and operate close to the rate of hybridization.
Collapse
Affiliation(s)
- Dalu Chang
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| |
Collapse
|
26
|
Werther P, Möhler JS, Wombacher R. A Bifunctional Fluorogenic Rhodamine Probe for Proximity-Induced Bioorthogonal Chemistry. Chemistry 2017; 23:18216-18224. [DOI: 10.1002/chem.201703607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Jasper S. Möhler
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| |
Collapse
|
27
|
O’Reilly RK, Turberfield AJ, Wilks TR. The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery. Acc Chem Res 2017; 50:2496-2509. [PMID: 28915003 PMCID: PMC5746846 DOI: 10.1021/acs.accounts.7b00280] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Precise control over reactivity and molecular
structure is a fundamental
goal of the chemical sciences. Billions of years of evolution by natural
selection have resulted in chemical systems capable of information
storage, self-replication, catalysis, capture and production of light,
and even cognition. In all these cases, control over molecular structure
is required to achieve a particular function: without structural control,
function may be impaired, unpredictable, or impossible. The
search for molecules with a desired function is often achieved
by synthesizing a combinatorial library, which contains many or all
possible combinations of a set of chemical building blocks (BBs),
and then screening this library to identify “successful”
structures. The largest libraries made by conventional synthesis are
currently of the order of 108 distinct molecules. To put
this in context, there are 1013 ways of arranging the 21
proteinogenic amino acids in chains up to 10 units long. Given that
we know that a number of these compounds have potent biological activity,
it would be highly desirable to be able to search them all to identify
leads for new drug molecules. Large libraries of oligonucleotides
can be synthesized combinatorially and translated into peptides using
systems based on biological replication such as mRNA display, with
selected molecules identified by DNA sequencing; but these methods
are limited to BBs that are compatible with cellular machinery. In
order to search the vast tracts of chemical space beyond nucleic acids
and natural peptides, an alternative approach is required. DNA-templated
synthesis (DTS) could enable us to meet this challenge.
DTS controls chemical product formation by using the specificity of
DNA hybridization to bring selected reactants into close proximity,
and is capable of the programmed synthesis of many distinct products
in the same reaction vessel. By making use of dynamic, programmable
DNA processes, it is possible to engineer a system that can translate
instructions coded as a sequence of DNA bases into a chemical structure—a
process analogous to the action of the ribosome in living organisms
but with the potential to create a much more chemically diverse set
of products. It is also possible to ensure that each product molecule
is tagged with its identifying DNA sequence. Compound libraries synthesized
in this way can be exposed to selection against suitable targets,
enriching successful molecules. The encoding DNA can then be amplified
using the polymerase chain reaction and decoded by DNA sequencing.
More importantly, the DNA instruction sequences can be mutated and
reused during multiple rounds of amplification, translation, and selection.
In other words, DTS could be used as the foundation for a system of
synthetic molecular evolution, which could allow us to efficiently
search a vast chemical space. This has huge potential to revolutionize
materials discovery—imagine being able to evolve molecules
for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety
of reactions can be performed on a DNA template. Complex architectures
and autonomous “DNA robots” have been implemented for
the controlled assembly of BBs, and these mechanisms have in turn
enabled the one-pot synthesis of large combinatorial libraries. Indeed,
DTS libraries are being exploited by pharmaceutical companies and
have already found their way into drug lead discovery programs. This
Account explores the processes involved in DTS and highlights the
challenges that remain in creating a general system for molecular
discovery by evolution.
Collapse
Affiliation(s)
- Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas R. Wilks
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
28
|
Petszulat H, Seitz O. A fluorogenic native chemical ligation for assessing the role of distance in peptide-templated peptide ligation. Bioorg Med Chem 2017; 25:5022-5030. [PMID: 28823838 DOI: 10.1016/j.bmc.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/19/2017] [Accepted: 08/06/2017] [Indexed: 12/11/2022]
Abstract
Protein-templated reactions have been used for fragment-based drug discovery as well as for covalent labeling, detection and manipulation of proteins. In spite of the growing interest in protein-templated reactions, little is known about the design criteria. Herein we present a systematic study on the effects of proximity in peptide-templated reactions. To facilitate reaction monitoring at low concentrations we developed a fluorogenic native chemical ligation that is based on the integration of a fluorescence quencher in the thiol leaving group. The reaction system provided up to 39-fold increases of emission from a fluorescein unit. By using templates based on coiled coils as models we investigated the effect of misalignments. The distance-reactivity pattern for remotely aligned peptides was remarkably different to reaction scenarios that involved seamlessly annealed peptides with overhanging functional groups.
Collapse
Affiliation(s)
- Henrik Petszulat
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Oliver Seitz
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| |
Collapse
|
29
|
Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
Collapse
Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| |
Collapse
|
30
|
Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017; 56:5247-5251. [PMID: 28382640 PMCID: PMC5502887 DOI: 10.1002/anie.201701356] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm.
Collapse
Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jason Y H Chang
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| |
Collapse
|
31
|
Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Jason Y. H. Chang
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Sylvain Ladame
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| |
Collapse
|
32
|
Di Pisa M, Hauser A, Seitz O. Maximizing Output in RNA-Programmed Peptidyl-Transfer Reactions. Chembiochem 2017; 18:872-879. [PMID: 28106939 DOI: 10.1002/cbic.201600687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 01/10/2023]
Abstract
A chemical reaction that is triggered by a specific RNA molecule might provide opportunities for the design of artificial feedback loops. We envision a peptidyl transfer reaction in which mRNA encoding an antiapoptotic protein would instruct the synthesis of apoptosis-inducing peptides. In this study, we used the RNA-programmed synthesis of a 16-mer peptide derived from the BH3 domain of the protein Bak, which inhibits the antiapoptotic protein Bcl-xL . The reaction involves the transfer of a thioester-linked donor peptide fragment from one PNA conjugate to an acceptor peptide-PNA conjugate. We asked two key questions. What are the chemical requirements that allow RNA-templated synthesis of a 16-mer peptide to proceed at lower (nanomolar) concentrations of RNA, that is, the concentration range found in cancer cells? Will such reactions provide sufficient amounts of peptide product and sufficient affinity to interfere with the targeted protein-protein interaction? Perhaps surprisingly, the lengths of the peptides involved in peptidyl transfer chemistry have little effect on the achievable rate enhancements. However, the nature of the thioester C terminus, the distance between the targeted template annealing sites, and template affinity play important roles. The investigation revealed guidelines for the reaction design for peptidyl transfer with low amounts (1-10 nm) of RNA, yet still provide sufficient product to antagonize a protein-protein interaction.
Collapse
Affiliation(s)
- Margherita Di Pisa
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
| | - Anett Hauser
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
| |
Collapse
|
33
|
Chang D, Lindberg E, Winssinger N. Critical Analysis of Rate Constants and Turnover Frequency in Nucleic Acid-Templated Reactions: Reaching Terminal Velocity. J Am Chem Soc 2017; 139:1444-1447. [DOI: 10.1021/jacs.6b12764] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| |
Collapse
|
34
|
Oliver Seitz. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/anie.201600985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
Oliver Seitz. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
36
|
Lotze J, Reinhardt U, Seitz O, Beck-Sickinger AG. Peptide-tags for site-specific protein labelling in vitro and in vivo. MOLECULAR BIOSYSTEMS 2016; 12:1731-45. [DOI: 10.1039/c6mb00023a] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide-tag based labelling can be achieved by (i) enzymes (ii) recognition of metal ions or small molecules and (iii) peptide–peptide interactions and enables site-specific protein visualization to investigate protein localization and trafficking.
Collapse
Affiliation(s)
- Jonathan Lotze
- Institut für Biochemie
- Universität Leipzig
- D-04103 Leipzig
- Germany
| | - Ulrike Reinhardt
- Institut für Chemie
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | - Oliver Seitz
- Institut für Chemie
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | | |
Collapse
|
37
|
Reinhardt U, Lotze J, Mörl K, Beck-Sickinger AG, Seitz O. Rapid Covalent Fluorescence Labeling of Membrane Proteins on Live Cells via Coiled-Coil Templated Acyl Transfer. Bioconjug Chem 2015; 26:2106-17. [PMID: 26367072 DOI: 10.1021/acs.bioconjchem.5b00387] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescently labeled proteins enable the microscopic imaging of protein localization and function in live cells. In labeling reactions targeted against specific tag sequences, the size of the fluorophore-tag is of major concern. The tag should be small to prevent interference with protein function. Furthermore, rapid and covalent labeling methods are desired to enable the analysis of fast biological processes. Herein, we describe the development of a method in which the formation of a parallel coiled coil triggers the transfer of a fluorescence dye from a thioester-linked coil peptide conjugate onto a cysteine-modified coil peptide. This labeling method requires only small tag sequences (max 23 aa) and occurs with high tag specificity. We show that size matching of the coil peptides and a suitable thioester reactivity allow the acyl transfer reaction to proceed within minutes (rather than hours). We demonstrate the versatility of this method by applying it to the labeling of different G-protein coupled membrane receptors including the human neuropeptide Y receptors 1, 2, 4, 5, the neuropeptide FF receptors 1 and 2, and the dopamine receptor 1. The labeled receptors are fully functional and able to bind the respective ligand with high affinity. Activity is not impaired as demonstrated by activation, internalization, and recycling experiments.
Collapse
Affiliation(s)
- Ulrike Reinhardt
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| | - Jonathan Lotze
- Institut für Biochemie, Universität Leipzig , Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Karin Mörl
- Institut für Biochemie, Universität Leipzig , Brüderstrasse 34, D-04103 Leipzig, Germany
| | | | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| |
Collapse
|
38
|
Barluenga S, Winssinger N. PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions. Acc Chem Res 2015; 48:1319-31. [PMID: 25947113 DOI: 10.1021/acs.accounts.5b00109] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The programmability of oligonucleotide hybridization offers an attractive platform for the design of assemblies with emergent properties or functions. Developments in DNA nanotechnologies have transformed our thinking about the applications of nucleic acids. Progress from designed assemblies to functional outputs will continue to benefit from functionalities added to the nucleic acids that can participate in reactions or interactions beyond hybridization. In that respect, peptide nucleic acids (PNAs) are interesting because they combine the hybridization properties of DNA with the modularity of peptides. In fact, PNAs form more stable duplexes with DNA or RNA than the corresponding natural homoduplexes. The high stability achieved with shorter oligomers (an 8-mer is sufficient for a stable duplex at room temperature) typically results in very high sequence fidelity in the hybridization with negligible impact of the ionic strength of the buffer due to the lack of electrostatic repulsion between the duplex strands. The simple peptidic backbone of PNA has been shown to be tolerant of modifications with substitutions that further enhance the duplex stability while providing opportunities for functionalization. Moreover, the metabolic stability of PNAs facilitates their integration into systems that interface with biology. Over the past decade, there has been a growing interest in using PNAs as biosupramolecular tags to program assemblies and reactions. A series of robust templated reactions have been developed with functionalized PNA. These reactions can be used to translate DNA templates into functional polymers of unprecedented complexity, fluorescent outputs, or bioactive small molecules. Furthermore, cellular nucleic acids (mRNA or miRNA) have been harnessed to promote assemblies and reactions in live cells. The tolerance of PNA synthesis also lends itself to the encoding of small molecules that can be further assembled on the basis of their nucleic acid sequences. It is now well-established that hybridization-based assemblies displaying two or more ligands can interact synergistically with a target biomolecule. These assemblies have now been shown to be functional in vivo. Similarly, PNA-tagged macromolecules have been used to prepare bioactive assemblies and three-dimensional nanostructures. Several technologies based on DNA-templated synthesis of sequence-defined polymers or DNA-templated display of ligands have been shown to be compatible with reiterative cycles of selection/amplification starting with large libraries of DNA templates, bringing the power of in vitro evolution to synthetic molecules and offering the possibility of exploring uncharted molecular diversity space with unprecedented scope and speed.
Collapse
Affiliation(s)
- Sofia Barluenga
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| |
Collapse
|
39
|
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
| |
Collapse
|
40
|
Schmalisch J, Seitz O. Acceleration of thiol additive-free native chemical ligation by intramolecular S → S acyl transfer. Chem Commun (Camb) 2015; 51:7554-7. [DOI: 10.1039/c5cc01447f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The old dog and a new trick; mercaptopropionylcysteine (MPA–Cys) peptide thioesters show a surprisingly high reactivity in native chemical ligation (NCL) and allow thiol-additive free reactions. This facilitates sequential NCL reactions and ligation–desulfurization reactions in one-pot formats. The synthetic utility is demonstrated by the synthesis of a SH3 domain.
Collapse
Affiliation(s)
- J. Schmalisch
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin
- Germany
| | - O. Seitz
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin
- Germany
| |
Collapse
|
41
|
Wu H, Cisneros BT, Cole C, Devaraj NK. Bioorthogonal tetrazine-mediated transfer reactions facilitate reaction turnover in nucleic acid-templated detection of microRNA. J Am Chem Soc 2014; 136:17942-5. [PMID: 25495860 PMCID: PMC4291768 DOI: 10.1021/ja510839r] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 12/17/2022]
Abstract
Tetrazine ligations have proven to be a powerful bioorthogonal technique for the detection of many labeled biomolecules, but the ligating nature of these reactions can limit reaction turnover in templated chemistry. We have developed a transfer reaction between 7-azabenzonorbornadiene derivatives and fluorogenic tetrazines that facilitates turnover amplification of the fluorogenic response in nucleic acid-templated reactions. Fluorogenic tetrazine-mediated transfer (TMT) reaction probes can be used to detect DNA and microRNA (miRNA) templates to 0.5 and 5 pM concentrations, respectively. The endogenous oncogenic miRNA target mir-21 could be detected in crude cell lysates and detected by imaging in live cells. Remarkably, the technique is also able to differentiate between miRNA templates bearing a single mismatch with high signal to background. We imagine that TMT reactions could find wide application for amplified fluorescent detection of clinically relevant nucleic acid templates.
Collapse
Affiliation(s)
- Haoxing Wu
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Brandon T. Cisneros
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Christian
M. Cole
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| |
Collapse
|
42
|
Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
Collapse
Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
| | | | | | | | | | | | | |
Collapse
|
43
|
He Y, Chen D, Li M, Fang L, Yang W, Xu L, Fu F. Rolling circle amplification combined with gold nanoparticles-tag for ultra sensitive and specific quantification of DNA by inductively coupled plasma mass spectrometry. Biosens Bioelectron 2014; 58:209-13. [DOI: 10.1016/j.bios.2014.02.072] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/16/2022]
|
44
|
Reinhardt U, Lotze J, Zernia S, Mörl K, Beck-Sickinger AG, Seitz O. Proteintemplat-vermittelter Acyltransfer: eine chemische Methode für die Markierung von Membranproteinen an lebenden Zellen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
45
|
Reinhardt U, Lotze J, Zernia S, Mörl K, Beck-Sickinger AG, Seitz O. Peptide-Templated Acyl Transfer: A Chemical Method for the Labeling of Membrane Proteins on Live Cells. Angew Chem Int Ed Engl 2014; 53:10237-41. [DOI: 10.1002/anie.201403214] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 12/22/2022]
|
46
|
Patzke V, McCaskill JS, von Kiedrowski G. DNA mit 3′-5′-Disulfid-Verknüpfung - schnelle chemische Ligation durch isosteren Ersatz. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
47
|
Patzke V, McCaskill JS, von Kiedrowski G. DNA with 3'-5'-disulfide links--rapid chemical ligation through isosteric replacement. Angew Chem Int Ed Engl 2014; 53:4222-6. [PMID: 24623660 DOI: 10.1002/anie.201310644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Efforts to chemically ligate oligonucleotides, without resorting to biochemical enzymes, have led to a multitude of synthetic analogues, and have extended oligomer ligation to reactions of novel oligonucleotides, peptides, and hybrids such as PNA.1 Key requirements for potential diagnostic tools not based on PCR include a fast templated chemical DNA ligation method that exhibits high pairing selectivity, and a sensitive detection method. Here we report on a solid-phase synthesis of oligonucleotides containing 5'- or 3'-mercapto-dideoxynucleotides and their chemical ligations, yielding 3'-5'-disulfide bonds as a replacement for 3'-5'-phosphodiester units. Employing a system designed for fluorescence monitoring, we demonstrate one of the fastest ligation reactions with half-lives on the order of seconds. The nontemplated ligation reaction is efficiently suppressed by the choice of DNA modification and the 3'-5' orientation of the activation site. The influence of temperature on the templated reaction is shown.
Collapse
Affiliation(s)
- Volker Patzke
- Lehrstuhl für Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany).
| | | | | |
Collapse
|
48
|
Vázquez O, Seitz O. Templated native chemical ligation: peptide chemistry beyond protein synthesis. J Pept Sci 2014; 20:78-86. [PMID: 24395765 DOI: 10.1002/psc.2602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 12/11/2022]
Abstract
Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.
Collapse
Affiliation(s)
- Olalla Vázquez
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| |
Collapse
|
49
|
Vázquez O, Seitz O. Cytotoxic peptide–PNA conjugates obtained by RNA-programmed peptidyl transfer with turnover. Chem Sci 2014. [DOI: 10.1039/c4sc00299g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A RNA triggered chemical peptidyl transfer reaction leads to a cytotoxic peptide conjugate that requires turnover in RNA for bioactivity.
Collapse
Affiliation(s)
- O. Vázquez
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - O. Seitz
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| |
Collapse
|
50
|
Michaelis J, Roloff A, Seitz O. Amplification by nucleic acid-templated reactions. Org Biomol Chem 2014; 12:2821-33. [DOI: 10.1039/c4ob00096j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acid-templated reactions that proceed with turnover provide a means for signal amplification, which facilitates the use and detection of biologically occurring DNA/RNA molecules.
Collapse
Affiliation(s)
- Julia Michaelis
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Alexander Roloff
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| |
Collapse
|