Alexander Deiters

Alexander Deiters
University of Pittsburgh | Pitt · Department of Chemistry

PhD

About

234
Publications
23,343
Reads
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11,739
Citations
Additional affiliations
September 2013 - present
University of Pittsburgh
Position
  • Professor
August 2004 - August 2013
North Carolina State University
Position
  • Research Assistant
July 2002 - July 2004
The Scripps Research Institute
Position
  • PostDoc Position

Publications

Publications (234)
Article
Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatu...
Article
DNA computation can utilize logic gates as modules to create molecular computers with biological inputs. Modular circuits that recognize nucleic acid inputs through strand hybridization activate computation cascades to produce controlled outputs. This allows for the construction of synthetic circuits that can be interfaced with cellular environment...
Article
Full-text available
MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene regulators and have been shown to regulate many biological processes including embryonal development, cell differentiation, apoptosis, and proliferation. Variations in the expression of certain miRNAs have been linked to a wide range of human diseases - especially ca...
Article
A highly convergent synthesis of the pyridine core of the thiopeptide antibiotic cyclothiazomycin has been developed based on a [2+2+2] cyclotrimerization key step. The regioselective assembly of the heterocyclic center of this important class of antibiotics takes advantage of a temporary silicon tether and the ruthenium-catalyzed cyclotrimerizatio...
Article
Cre recombinase catalyzes DNA exchange between two conserved lox recognition sites. The enzyme has extensive biological application, from basic cloning to engineering knock-out and knock-in organisms. Widespread use of Cre is due to its simplicity and effectiveness, but the enzyme and the recombination event remain difficult to control with high pr...
Article
MicroRNAs play crucial and dynamic roles in vertebrate development and diseases. Some, like miR-430, are highly expressed during early embryo development and regulate hundreds of transcripts, which can make it difficult to study their role in the timing and location of specific developmental processes using conventional morpholino oligonucleotide (...
Article
Many proteins harboring low complexity or intrinsically disordered sequences (IDRs) are capable of undergoing liquid-liquid phase separation to form mesoscale condensates that function as biochemical niches with the ability to concentrate or sequester macromolecules and regulate cellular activity. Engineered disordered proteins have been used to ge...
Preprint
A wide array of optogenetic tools is available that allow for precise spatiotemporal control over many cellular processes. These tools have been especially popular among zebrafish researchers who take advantage of the embryo's transparency. However, photocleavable optogenetic proteins have not been utilized in zebrafish. We demonstrate successful o...
Article
Full-text available
Despite their low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival in h...
Article
Cells utilize protein translocation to specific compartments for spatial and temporal regulation of protein activity, in particular in the context of signaling processes. Protein recognition and binding to various subcellular membranes is mediated by a network of phosphatidylinositol phosphate (PIP) species bearing one or multiple phosphate moietie...
Article
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of ext...
Article
Full-text available
Chemically induced dimerization of FKBP and FRB using rapamycin and rapamycin analogs has been utilized in a variety of biological applications. Formation of the FKBP-rapamycin-FRB ternary complex is typically used to activate a biological process and this interaction has proven to be essentially irreversible. In many cases, it would be beneficial...
Article
Full-text available
Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle pla...
Article
We developed a method to control gene activation and base editing in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs. Four evenly distributed, caged nucleobases are installed in the 5’‐protospacer region of the gRNA to block interaction between the dCas9:gRNA complex and the dsDNA target. Upon light activation,...
Article
Post-translational modifications (PTMs) of proteins extensively diversify the biological information flow from the genome to the proteome and thus have profound pathophysiological implications. Precise dissection of the regulatory networks of PTMs benefits from the ability to achieve conditional control through external optogenetic or chemogenetic...
Preprint
Full-text available
Despite their comparatively low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival, and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and thei...
Preprint
Despite their comparatively low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival, and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and thei...
Article
We developed a new approach to selectively modify native proteins in their biological environment using electrophilic, covalent aptamers. These aptamers are generated through introduction of a proximity‐driven electrophile at specific nucleic acid sites. Using thrombin as a proof‐of‐concept, we demonstrate that covalent aptamers can selectively tra...
Article
Full-text available
Due to their high stability and specificity in living cells, fluorescently labeled nanobodies are perfect probes for visualizing intracellular targets at an endogenous level. However, intrabodies bind unrestrainedly and hence may interfere with the target protein function. Here, we report a strategy to prevent premature binding through the developm...
Article
Nucleic acid aptamers were developed that are capable of covalently labeling their protein target with a functional molecule. Additionally, with little modification, the aptamer covalently crosslinked to its target instead, thereby inhibiting its function. Covalent aptamers offer a new tool for selective protein modification, detection, and inhibit...
Article
Sea urchins and other echinoderms are important experimental models for analyzing embryonic development, but a lack of spatial and temporal control over gene perturbations has hindered developmental studies using these animals. Morpholino antisense oligonucleotides (MOs) have been used successfully by the echinoderm research community for almost tw...
Article
Light-induced lysis of red blood cell carriers provides a delivery strategy for protein therapeutics with spatiotemporal control.
Article
Full-text available
Controlling unmodified serotonin levels in brain synapses is a primary objective when treating major depressive disorder — a disease that afflicts ~20% of the world’s population. Roughly 60% of patients respond poorly to first-line treatments and thus new therapeutic strategies are sought. Toward this end, we have constructed isoform-specific inhib...
Article
Full-text available
High-throughput matrix-assisted laser desorption/ionization mass spectrometry (HT-MALDI-MS) has garnered considerable attention within the drug discovery industry as an information-rich alternative to assays using light-based detection methods. To date, these efforts have been primarily focused on assays using protein or peptide substrates. Methods...
Article
Genetic code expansion with unnatural amino acids (UAAs) has significantly broadened the chemical repertoire of proteins. Applications of this method in mammalian cells include probing of molecular interactions, conditional control of biological processes, and new strategies for therapeutics and vaccines. A number of methods have been developed for...
Article
Conditional control of CRISPR/Cas9 has been developed using a variety of different approaches, many focusing on manipulation of the Cas9 protein itself. However, more recent strategies for governing CRISPR/Cas9 function are based on guide RNA (gRNA) modifications. They include control of gRNAs by light, small molecules, proteins, and oligonucleotid...
Preprint
Full-text available
DNA-based Boolean logic gates (AND, OR and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits diffi...
Article
Full-text available
Protein phosphatases play an essential role in cell signaling; however, they remain understudied compared with protein kinases, in part due to a lack of appropriate tools. In order to provide conditional control over phosphatase function, we developed two different approaches for rendering MKP3 (a dual-specific phosphatase, also termed DUSP6) activ...
Article
Full-text available
The selective pressure imposed by extrinsic death signals and stressors adds to the challenge of isolating and interpreting the roles of proteins in stress-activated signaling networks. By expressing a kinase with activating mutations and a caged lysine blocking the active site, we can rapidly switch on catalytic activity with light and monitor the...
Chapter
Effective, general methods for conditionally activating proteins in their native biological environments are highly useful for biological studies. Since phosphines and azides are not found in pro- and eukaryotic cells, the Staudinger reduction can function as an excellent small molecule-controlled switch for protein activation. This methodology inv...
Article
We developed a new tool for optical control of cellular ATP concentrations with a photocaged adenylate kinase (Adk). The photocaged Adk is generated by substituting a catalytically essential lysine with a hydroxycoumarin-protected lysine through site-specific unnatural amino acid mutagenesis in both E. coli and mammalian cells. Caging of the critic...
Article
A light‐activated gRNA allows for precise spatiotemporal control of gene editing by CRISPR/Cas9 in both mammalian cells and zebrafish embryos, with excellent off‐to‐on switching. This highly programmable approach can be easily adapted to any desired target sequence and can be delivered to a variety of organisms in the form of ribonucleoprotein comp...
Article
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs. Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’‐protospacer region with caged nucleobases during synthesis. Caging confers complete sup...
Preprint
Full-text available
Chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors are engineered cell-surface receptors that sense a target antigen and respond by activating T cell receptor signaling or a customized gene program, respectively. To expand the targeting capabilities of these receptors, we have developed switchable adaptor receptor systems fo...
Article
As an emerging approach to protein perturbation, small molecule-induced protein degradation has gained significant attention as both a chemical tool and a potential therapeutic. To enable discreet con-trol over its function, we have developed a broadly applicable approach for the optical activation of small molecule-induced protein degradation. By...
Article
The Staudinger reduction provides a bio‐orthogonal and generalizable approach to small‐molecule‐triggered protein activation. We have developed three genetically encoded caged lysine analogues that can be rapidly activated with phosphines in order to control protein function in mammalian cells. This was applied to the conditional control of protein...
Preprint
Full-text available
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs. Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5'-protospacer region with caged nucleobases during synthesis. Caging confers complete sup...
Article
In this issue of Cell Chemical Biology, the Sterner lab reports the application of photoswitchable unnatural amino acids in controlling protein allostery in the enzyme complex imidazole glycerol phosphate synthase (Kneuttinger et al., 2019). Remarkable switching in enzyme activity was achieved upon photoisomerization of an azobenzene amino acid. In...
Article
The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small‐molecule triggers that turn on proteins through a Staudinger reduction/self‐immolation cascade with substantially improved kinetics and yields. We achieved this through site‐specific incorporation...
Article
Rapamycin-induced dimerization of FKBP and FRB has been utilized as a tool for co-localizing two proteins of interest in numerous applications. Due to the tight binding interaction of rapamycin with FKBP and FRB, the ternary complex formation is essentially irreversible. Since biological processes occur in a highly dynamic fashion with cycles of pr...
Article
Full-text available
Protein phosphatases are involved in embryonic development, metabolic homeostasis, stress response, cell cycle transitions, and many other essential biological mechanisms. Unlike kinases, protein phosphatases remain understudied and less characterized. Traditional genetic and biochemical methods have contributed significantly to our understanding;...
Article
Many biological processes are naturally regulated with spatiotemporal control. In order to perturb and investigate them, optochemical tools have been developed that convey similar spatiotemporal precision. Pivotal to optochemical probes are photolabile protecting groups, so called caging groups, and recent developments have enabled new applications...
Preprint
Full-text available
p>As an emerging approach to protein perturbation, small molecule-induced protein degradation has gained significant attention as both a chemical tool and a potential therapeutic. To enable discreet spatiotemporal control over its activity, we have developed a broadly applicable approach for the optical control of small molecule-induced protein deg...
Chapter
MicroRNAs (miRNAs) are small, non-coding RNAs that predominantly regulate gene expression via translational repression. Dysregulation of miRNAs has been linked to various human diseases, including cancer, suggesting that targeting miRNAs with small molecules may hold therapeutic potential. As such, several approaches have been employed in order to...
Article
MicroRNAs (miRNAs) are short, non-coding RNA molecules estimated to regulate expression of a large number of protein-coding genes and are implicated in a variety of biological processes such as development, differentiation, proliferation, and cell survival. Dysregulation of miRNAs has been attributed to the onset and progression of various human di...
Article
Full-text available
Class I phosphoinositide 3-OH kinase (PI3K) signaling is central to animal growth and metabolism, and pathological disruption of this pathway affects cancer and diabetes. However, the specific spatial/temporal dynamics and signaling roles of its minor lipid messenger, phosphatidylinositol (3,4)-bisphosphate (PI(3,4)P 2 ), are not well understood. T...
Article
Full-text available
Engineered small molecule triggers are important tools for the control and investigation of biological processes, in particular protein function. Staudinger reductions of aryl azides to amines through the use of phosphines can trigger an elimination reaction, and thereby activation of a functional molecule, if an appropriately positioned leaving gr...
Chapter
Caged morpholino oligonucleotides (cMOs) are useful research tools in developmental biology because they allow spatiotemporal control of gene expression in whole organisms. While cMOs are usually triggered by light of a single wavelength, the introduction of spectrally distinct chromophores can enable combinatorial regulation of multiple genes. Thi...
Chapter
Cre recombinase-mediated DNA recombination is an established method for conditional control of gene expression in animal models. Regulation of its activity has been accomplished to impart spatial and/or temporal control over recombination of the target gene. In this chapter, optical control of Cre recombinase in developing zebrafish embryos through...
Article
Full-text available
Catecholamine neurotransmitter levels in the synapses of the brain shape human disposition— cognitive flexibility, aggression, depression, and reward seeking—and manipulating these levels is a major objective of the pharmaceutical industry. Certain neurotransmitters are extensively sulfonated and inactivated by human sulfotransferase 1A3 (SULT1A3)....
Article
Full-text available
Controlling protein activity with chemogenetics and optogenetics has proven to be powerful for testing hypotheses regarding protein function in rapid biological processes. Controlling proteins by splitting them and then rescuing their activity through inducible reassembly offers great potential to control diverse protein activities. Building split...
Article
The genetic encoding of three different azobenzene phenylalanines with different photochemical properties was achieved in human cells by using an engineered pyrrolysyl tRNA/tRNA synthetase pair. In order to demonstrate reversible light control of protein function, azobenzenes were site‐specifically introduced into firefly luciferase. Computational...
Article
Full-text available
The front cover picture shows the reversible optical switching of protein function through site‐specific incorporation of different azobenzene‐modified phenylalanines into proteins in cells with an expanded genetic code. The photochemical properties, such as excitation wavelengths and half‐life of the cis isomer, of the optical switches were tuned...
Preprint
Full-text available
Class I PI 3-kinase (PI3K) signaling is central to animal growth and metabolism, and disruption of this pathway occurs frequently in cancer and diabetes. However, the specific spatial/temporal dynamics and signaling roles of its minor lipid messenger, phosphatidylinositol (3,4)-bisphosphate [PI(3,4)P2], are not well understood. This owes principall...
Article
This manuscript describes a diverted total synthesis effort that is designed to prepare potent cytotoxins based on the actin‐binding natural product bistramide A. The major focus of this study is the preparation of analogs that contain oxygenation at the C29 position, which is necessary for a key reaction in the sequence but is not present in the n...
Article
Expanding the genetic code to enable the incorporation of unnatural amino acids into proteins in biological systems provides a powerful tool to study protein structure and function. While this technology has been mostly developed and applied in bacterial and mammalian cells, it recently expanded into animals, including worms, fruit flies, zebrafish...
Article
In nature, biological processes are regulated with precise spatial and temporal resolution at the molecular, cellular, and organismal levels. In order to perturb and manipulate these processes, optically controlled chemical tools have been developed and applied in living systems. The use of light as an external trigger provides spatial and temporal...
Article
Chemical probes of microRNA (miRNA) function are potential tools for understanding miRNA biology that also provide new approaches for discovering therapeutics for miRNA-associated diseases. MicroRNA-21 (miR-21) is an oncogenic miRNA that is overexpressed in most cancers and has been strongly associated with driving chemoresistance in cancers such a...
Article
Full-text available
Diverse optochemical and optobiological approaches are being developed and applied to the light‐regulation of cellular processes with exquisite spatial and temporal resolution in cells and multicellular model organisms. In this special issue, experts report some of the latest progress in the expanding field of the optical control of biological syst...
Article
Cell lineage tracing is used to study embryo development, stem cell differentiation, and to document tumor cell heterogeneity. Cre recombinase‐mediated cell labelling is the preferred approach; however, its utility is restricted by when and where DNA recombination takes place. We generated a photoactivatable Cre recombinase by replacing a critical...
Article
We report inducible dimerization strategies for controlling protein positioning, enzymatic activity, and organelle assembly inside synthetic cell-like compartments upon photostimulation. Using a photocaged TMP-Haloligand compound, we demonstrate small molecule and light-induced dimerization of DHFR and Haloenzyme to localize proteins to a compartme...
Article
DNA-based logic gates can be assembled into computational devices that generate a specific output signal in response to oligonucleotide input patterns. The ability to interface with biological and chemical environments makes DNA computation a promising technology for monitoring cellular systems. However, DNA logic gate circuits typically provide a...
Article
Site-specific incorporation of unnatural amino acids into proteins provides a powerful tool to study protein function. Here we report genetic code expansion in zebrafish embryos and its application to the optogenetic control of cell signaling. We genetically encoded four unnatural amino acids with a diverse set of functional groups, which included...
Article
We genetically encoded three new caged tyrosine analogues with improved photochemical properties by using an engineered pyrrolysyl-tRNA synthetase/tRNACUA pair in bacterial and mammalian cells. We applied the new tyrosine analogues to the photoregulation of firefly luciferase by caging its key tyrosine residue, Tyr340, and observed excellent off-to...
Article
Achieving precise control of biological function represents a crucial tool for studying the mechanisms of cellular processes. Naturally, these processes occur in a strict spatially and temporally regulated fashion. In order to generate accurate models, the tools used to study these processes must also operate with high spatiotemporal resolution. To...
Article
Achieving precise control of biological function represents a crucial tool for studying the mechanisms of cellular processes. Naturally, these processes occur in a strict spatially and temporally regulated fashion. In order to generate accurate models, the tools used to study these processes must also operate with high spatiotemporal resolution. To...
Article
Full-text available
Nucleotide excision repair (NER) is a general DNA repair mechanism that is capable of removing a wide variety of DNA lesions induced by physical or chemical insults. UvrD, a member of the helicase SF1 superfamily, plays an essential role in bacterial NER by unwinding the duplex DNA in the 3' to 5' direction to displace the lesion-containing strand....