1
|
Govindarajan A, Gnanasambandam V. Toward Intracellular Bioconjugation Using Transition-Metal-Free Techniques. Bioconjug Chem 2021; 32:1431-1454. [PMID: 34197073 DOI: 10.1021/acs.bioconjchem.1c00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bioconjugation is the chemical strategy of covalent modification of biomolecules, using either an external reagent or other biomolecules. Since its inception in the twentieth century, the technique has grown by leaps and bounds, and has a variety of applications in chemical biology. However, it is yet to reach its full potential in the study of biochemical processes in live cells, mainly because the bioconjugation strategies conflict with cellular processes. This has mostly been overcome by using transition metal catalysts, but the presence of metal centers limit them to in vitro use, or to the cell surface. These hurdles can potentially be circumvented by using metal-free strategies. However, the very modifications that are necessary to make such metal-free reactions proceed effectively may impact their biocompatibility. This is because biological processes are easily perturbed and greatly depend on the prevailing inter- and intracellular environment. With this taken into consideration, this review analyzes the applicability of the transition-metal-free strategies reported in this decade to the study of biochemical processes in vivo.
Collapse
Affiliation(s)
- Aaditya Govindarajan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
| | - Vasuki Gnanasambandam
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
| |
Collapse
|
2
|
Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
Collapse
Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
| | | | | |
Collapse
|
3
|
Büllmann SM, Jäschke A. Norbornadiene-bridged diarylethenes and their conversion into turn-off fluorescent photoswitches. Chem Commun (Camb) 2020; 56:7124-7127. [PMID: 32458841 DOI: 10.1039/d0cc02210a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis and characterization of novel diarylethene photoswitches that contain a norbornadiene bridge and operate as p-type positive photochromes. One of the double bonds of norbornadiene is furthermore utilized to attach a fluoresceine tetrazine by an iEDDA cascade reaction, thereby forming a turn-off mode fluorescent photoswitch.
Collapse
Affiliation(s)
- Simon M Büllmann
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
| | | |
Collapse
|
4
|
Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| |
Collapse
|
5
|
Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 655] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
Collapse
Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
| |
Collapse
|
6
|
Winz ML, Linder EC, Becker J, Jäschke A. Site-specific one-pot triple click labeling for DNA and RNA. Chem Commun (Camb) 2018; 54:11781-11784. [DOI: 10.1039/c8cc04520h] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report site-specific triple click labeling for DNA and RNA in a one-pot setup by performing inverse electron demand Diels–Alder reaction and strain-promoted and copper catalyzed click reactions sequentially.
Collapse
Affiliation(s)
- Marie-Luise Winz
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Eva Christina Linder
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Juliane Becker
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Andres Jäschke
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| |
Collapse
|
7
|
Muttach F, Muthmann N, Reichert D, Anhäuser L, Rentmeister A. A benzylic linker promotes methyltransferase catalyzed norbornene transfer for rapid bioorthogonal tetrazine ligation. Chem Sci 2017; 8:7947-7953. [PMID: 29619168 PMCID: PMC5858020 DOI: 10.1039/c7sc03631k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
Site-specific alkylation of complex biomolecules is critical for late-stage product diversification as well as post-synthetic labeling and manipulation of proteins and nucleic acids. Promiscuous methyltransferases in combination with analogs of S-adenosyl-l-methionine (AdoMet) can functionalize all major classes of biomolecules. We show that benzylic moieties are transferred by Ecm1 with higher catalytic efficiency than the natural AdoMet. A relative specificity of up to 80% is achieved when a norbornene moiety is placed in para-position, enabling for the first time enzymatic norbornene transfer to specific positions in DNA and RNA- even in cell lysate. Subsequent tetrazine ligation of the stable norbornene moiety is fast, efficient, biocompatible and - in combination with an appropriate tetrazine - fluorogenic.
Collapse
Affiliation(s)
- F Muttach
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - N Muthmann
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - D Reichert
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
| | - L Anhäuser
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - A Rentmeister
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
| |
Collapse
|
8
|
Ren X, El-Sagheer AH, Brown T. Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes. Nucleic Acids Res 2016; 44:e79. [PMID: 26819406 PMCID: PMC4856977 DOI: 10.1093/nar/gkw028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/11/2016] [Indexed: 12/12/2022] Open
Abstract
A sterically undemanding azide analogue of dTTP (AHP dUTP) with an alkyl chain and ethynyl attachment to the nucleobase was designed and incorporated into DNA by primer extension, reverse transcription and polymerase chain reaction (PCR). An azide-modified 523 bp PCR amplicon with all 335 thymidines replaced by AHP dU was shown to be a perfect copy of the template from which it was amplified. Replacement of thymidine with AHP dU increases duplex stability, accounting in part for the high incorporation efficiency of the azide-modified triphosphate. Single-stranded azide-labelled DNA was conveniently prepared from PCR products by λ-exonuclease digestion and streptavidin magnetic bead isolation. Efficient fluorescent labelling of single and double-stranded DNA was carried out using dyes functionalized with bicyclo[6.1.0]non-4-yne (BCN) via the strain-promoted alkyne-azide cycloaddition (SPAAC) reaction. This revealed that the degree of labelling must be carefully controlled to achieve optimum fluorescence and avoid fluorescence quenching. Dual-coloured probes were obtained in a single tube fluorescent labelling reaction; and varying the ratios of the two dyes provides a simple method to prepare DNA probes with unique fluorescent signatures. AHP dUTP is a versatile clickable nucleotide with potentially wide applications in biology and nanotechnology including single molecule studies and synthesis of modified aptamer libraries via SELEX.
Collapse
Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
9
|
Busskamp H, Batroff E, Niederwieser A, Abdel-Rahman OS, Winter RF, Wittmann V, Marx A. Efficient labelling of enzymatically synthesized vinyl-modified DNA by an inverse-electron-demand Diels-Alder reaction. Chem Commun (Camb) 2015; 50:10827-9. [PMID: 25089682 DOI: 10.1039/c4cc04332d] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many applications in biotechnology and molecular biology rely on modified nucleotides. Here, we present an approach for the postsynthetic labelling of enzymatically synthesized vinyl-modified DNA by Diels-Alder reaction with inverse electron demand using a tetrazine. Labelling proceeds very efficiently and supersedes several known approaches.
Collapse
Affiliation(s)
- Holger Busskamp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
| | | | | | | | | | | | | |
Collapse
|