Synthesis of fluorescent oligonucleotide--EYFP conjugate: towards supramolecular construction of semisynthetic biomolecular antennae

Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates

Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.

DNA-Directed Assembly of a Cell-Responsive Biohybrid Interface for Cargo Release

The development of a DNA-based cell-responsive biohybrid interface that can be used for spatially confined release of molecular cargo is reported. To this end, tailored DNA-protein conjugates are designed as gatekeepers that can be specifically cleaved by matrix metalloproteases (MMPs), which are secreted by many cancer cells. These gatekeepers can be installed by DNA hybridization on the surface of mesoporous silica nanoparticles (MSNs). The MSNs display another orthogonal DNA oligonucleotide that can be exploited for site-selective immobilization on solid glass surfaces to yield micropatterned substrates for cell adhesion. Using the human fibrosarcoma cell line HT1080 that secretes MMPs, it is demonstrated that the biohybrid surface is specifically modified by the cells to release both MSN-bound gatekeeper proteins and the encapsulated cargo peptide KLA. In view of the enormously high modularity of the system presented here, this approach promising for applications in drug delivery, tissue engineering, or other areas of nanobiotechnology is considered.

Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices

The design and construction of crystalline protein arrays to selectively assemble ordered nanoscale materials have potential applications in sensing, catalysis, and medicine. Whereas numerous designs have been implemented for the bottom-up construction of protein assemblies, the generation of artificial functional materials has been relatively unexplored. Enzyme-directed post-translational modifications are responsible for the functional diversity of the proteome and, thus, could be harnessed to selectively modify artificial protein assemblies. In this study, we describe the use of phosphopantetheinyl transferases (PPTases), a class of enzymes that covalently modify proteins using coenzyme A (CoA), to site-selectively tailor the surface of designed, two-dimensional (2D) protein crystals. We demonstrate that a short peptide (ybbR) or a molecular tag (CoA) can be covalently tethered to 2D arrays to enable enzymatic functionalization using Sfp PPTase. The site-specific modification of two different protein array platforms is facilitated by PPTases to afford both small molecule- and protein-functionalized surfaces with no loss of crystalline order. This work highlights the potential for chemoenzymatic modification of large protein surfaces toward the generation of sophisticated protein platforms reminiscent of the complex landscape of cell surfaces.

Efficient bioactive oligonucleotide-protein conjugation for cell-targeted cancer therapy

Oligonucleotide-protein conjugates have important applications in biomedicine. Simple and efficient methods are described for the preparation of these conjugates. Specifically, we describe a new method in which a bifunctional linker is attached to thiol-oligonucleotide to generate a reactive intermediate that is used to link to the protein. Having similar conjugation efficacy compared with the classical method in which the bifunctional linker is attached first to the protein, this new approach produces significantly more active conjugates with higher batch to batch reproducibility. In a second approach, direct conjugation is proposed using oligonucleotides carrying carboxyl groups. These methodologies have been applied to prepare nanoconjugates of an engineered nanoparticle protein carrying a T22 peptide with affinity for the CXCR4 chemokine receptor and oligomers of the antiproliferative nucleotide 2'-deoxy-5-fluorouridine in a very efficient way. The protocols have potential uses for the functionalization of proteins, amino-containing polymers or amino-lipids in order to produce complex therapeutic nucleic acid delivery systems.

Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions

The co-self-assembly of proteins and nucleic acids (NAs) produces complex biomolecular machines (e.g., ribosomes and telomerases) that represent some of the most daunting targets for biomolecular design. Despite significant advances in protein and DNA or RNA nanotechnology, the construction of artificial nucleoprotein complexes has largely been limited to cases that rely on the NA-mediated spatial organization of protein units, rather than a cooperative interplay between protein- and NA-mediated interactions that typify natural nucleoprotein assemblies. We report here a structurally well-defined synthetic nucleoprotein assembly that forms through the synergy of three types of intermolecular interactions: Watson-Crick base pairing, NA-protein interactions, and protein-metal coordination. The fine thermodynamic balance between these interactions enables the formation of a crystalline architecture under highly specific conditions.

Entirely enzymatic nanofabrication of DNA-protein conjugates

While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA–protein conjugates - offer the ability to combine the programmability of DNA with the competence of proteins to form novel tools enabling exquisite molecular control and the highest biological activity in one structure. However, in order for tools like these to become viable for biological applications, their production must be scalable, and an entirely enzymatic process is one way to achieve this. Here, we present a step in this direction: enzymatic production of DNA–protein conjugates using a new self-labeling tag derived from a truncated VirD2 protein of Agrobacterium tumefaciens. Using our previously reported MOSIC method for enzymatic ssDNA oligo production, we outline a pipeline for protein–DNA conjugates without the need for any synthetic chemistry in a one-pot reaction. Further, we validate HER2 staining using a completely enzymatically produced probe, enable the decoration of cell membranes and control of genetic expression. Establishing a method where protein–DNA conjugates can be made entirely using biological or enzymatic processing, opens a path to harvest these structures directly from bacteria and ultimately in-vivo assembly.

Super-Resolution Imaging Conditions for enhanced Yellow Fluorescent Protein (eYFP) Demonstrated on DNA Origami Nanorulers

Photostability is one of the crucial properties of a fluorophore which strongly influences the quality of single molecule-based super-resolution imaging. Enhanced yellow fluorescent protein (eYFP) is one of the most widely used versions of fluorescent proteins in modern cell biology exhibiting fast intrinsic blinking and reversible photoactivation by UV light. Here, we developed an assay for studying photostabilization of single eYFP molecules with respect to fast blinking and demonstrated a 6-fold enhanced photostability of single eYFP molecules with a beneficial influence on the blinking kinetics under oxygen removal and addition of aliphatic thiols (dSTORM-buffer). Conjugation to single stranded DNA and immobilization via DNA hybridization on a DNA origami 12 helix bundle in aqueous solution allowed photophyiscal studies of eYFP at the single-molecule level and at close to physiological conditions. The benefit of improved photophysical properties for localization-based super-resolution microscopy is demonstrated and quantitatively characterized by imaging 12 helix bundle DNA origami nanorulers with binding sites at designed distances of 160 and 100 nm and by imaging microtubules in fixed mammalian Vero cells.

Evidence of unfolded protein translocation through a protein nanopore

Protein nanopores are mainly used to study transport, unfolding, intrinsically disordered proteins, protein-pore interactions, and protein-ligand complexes. This single-molecule sensor for biomedical and biotechnological applications is promising but until now direct proof of protein translocation through a narrow channel is lacking. Here, we report the translocation of a chimera molecule through the aerolysin nanopore in the presence of a denaturing agent, guanidium chloride (1.5 M) and KCl (1 M). The chimera molecule is composed of the recombinant MalE protein with a unique cysteine residue at the C-terminal position covalently linked to a single-stranded DNA oligonucleotide. Real-time polymerase chain reaction (PCR) was used to detect the presence of chimera molecules that have been effectively translocated from the cis to trans chamber of the set up. Comparing the electrical signature of the chimera related to the protein or oligonucleotide alone demonstrates that each type of molecule displays different dynamics in term of transport time, event frequency, and current blockade. This original approach provides the possibility to study protein translocation through different biological, artificial, and biomimetic nanopores or nanotubes. New future applications are now conceivable such as protein refolding at the nanopore exit, peptides and protein sequencing, and peptide characterization for diagnostics.

Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet

A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.

Nano-scale alignment of proteins on a flexible DNA backbone

Nano-scale alignment of several proteins with freedom of motion is equivalent to an enormous increase in effective local concentration of proteins and will enable otherwise impossible weak and/or cooperative associations between them or with their ligands. For this purpose, a DNA backbone made of six oligodeoxynucleotide (ODN) chains is designed in which five double-stranded segments are connected by four single-stranded flexible linkers. A desired protein with an introduced cysteine is connected covalently to the 5'-end of azido-ODN by catalyst-free click chemistry. Then, six protein-ODN conjugates are assembled with their complementary nucleotide sequences into a single multi-protein-DNA complex, and six proteins are aligned along the DNA backbone. Flexible alignment of proteins is directly observed by high-speed AFM imaging, and association of proteins with weak interaction is demonstrated by fluorescence resonance energy transfer between aligned proteins.

Easy introduction of maleimides at different positions of oligonucleotide chains for conjugation purposes

[2,5-Dimethylfuran]-protected maleimides were placed at both internal positions and the 3'-end of oligonucleotides making use of solid-phase synthesis procedures. A new phosphoramidite derivative and a new solid support incorporating the protected maleimide moiety were prepared for this purpose. In all cases maleimide deprotection (retro-Diels-Alder reaction) followed by reaction with thiol-containing compounds afforded the target conjugate.

Advances in quantitative FRET-based methods for studying nucleic acids

Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.

Construction of semisynthetic DNA-protein conjugates with Phi X174 Gene-A* protein

DNA-protein conjugates have frequently been used as versatile molecular tools for a variety of applications in biotechnology to harness synergistic effects of DNA and protein functions. With applications for DNA-protein conjugates growing, easy-to-use and economical methods for the synthesis of DNA-protein conjugates are required. In this study, we developed a method for site-specific labeling of single-stranded DNA (ssDNA) to a recombinant protein of interest (POI) through the Gene-A* protein (Gene-A*) from bacteriophage phi X174, without any chemical modifications of ssDNA. Gene-A* protein is an enzyme that site-selectively cleaves an oligodeoxyribonucleotide (ODN) containing a Gene-A* recognition sequence, at which point a tyrosine residue of Gene-A* is bonded to the 5'-phosphoryl group of the cleavage site via a stable phosphotyrosine linkage. Here, we constructed three kinds of recombinant proteins fused to Gene-A*: N-terminally Gene-A*-fused enhanced green fluorescent protein (EGFP), C-terminally Gene-A*-fused EGFP, and N-terminally Gene-A*-fused firefly luciferase (FLuc). The reaction yields of DNA-protein conjugation catalyzed by the Gene-A* moiety reached 80-90% in the three proteins, and kinetic study revealed that the reaction achieved a steady state after 10 min. Moreover, dot blot analyses were performed to evaluate the hybridization and aptamer-forming ability of ssDNA conjugated to the Gene-A* moiety of a recombinant Gene-A*-FLuc protein. This study demonstrated that a strategy using recombinant proteins fused to Gene-A* could offer a versatile, rapid, easy-to-use, and economical platform for producing DNA-protein conjugates.

Orthogonal protein decoration of DNA nanostructures

The development of robust DNA-protein coupling techniques is mandatory for applications of DNA nanostructures in biomedical diagnostics, fundamental biochemistry, and other fields in biomolecular nanosciences. The use of self-labeling fusion proteins, which are orthogonal to biotin-streptavidin and antibody-antigen interactions, is described for the site-selective protein decoration of two exemplary DNA nanostructures: a four-way junction X-tile motif and a 3D DNA tetrahedron. Multifunctional DNA superstructures bearing up to four different proteins are generated and characterized by electrophoresis and microplate-based functionality assays. Steric and electrostatic interactions are identified as critical parameters controlling the efficiency of DNA-protein ligation. The results indicate that this method is versatile and broadly applicable, not only for the functionalization of DNA architectures but also for the site-specific decoration of other molecular materials and devices containing several different proteins.

Solid-state nanostructured materials from self-assembly of a globular protein-polymer diblock copolymer

Self-assembly of three-dimensional solid-state nanostructures containing approximately 33% by weight globular protein is demonstrated using a globular protein-polymer diblock copolymer, providing a route to direct nanopatterning of proteins for use in bioelectronic and biocatalytic materials. A mutant red fluorescent protein, mCherryS131C, was prepared by incorporation of a unique cysteine residue and site-specifically conjugated to end-functionalized poly(N-isopropylacrylamide) through thiol-maleimide coupling to form a well-defined model protein-polymer block copolymer. The block copolymer was self-assembled into bulk nanostructures by solvent evaporation from concentrated solutions. Small-angle X-ray scattering and transmission electron microscopy illustrated the formation of highly disordered lamellae or hexagonally perforated lamellae depending upon the selectivity of the solvent during evaporation. Solvent annealing of bulk samples resulted in a transition toward lamellar nanostructures with mCherry packed in a bilayer configuration and a large improvement in long-range ordering. Wide-angle X-ray scattering indicated that mCherry did not crystallize within the block copolymer nanodomains and that the β-sheet spacing was not affected by self-assembly. Circular dichroism showed no change in protein secondary structure after self-assembly, while UV-vis spectroscopy indicated approximately 35% of the chromophore remained optically active.

Maleimide-dimethylfuran exo adducts: effective maleimide protection in the synthesis of oligonucleotide conjugates

The reaction of maleimide-containing compounds with 2,5-dimethylfuran gives a mixture of exo and endo isomers from which the exo cycloadduct can be easily isolated taking advantage of its stability in concentrated aqueous ammonia. Bifunctional compounds incorporating a dimethylfuran-protected maleimide (exo adduct) have been attached to resin-linked oligonucleotide chains. Removal of protecting groups masking oligonucleotide functionalities followed by retro-Diels-Alder maleimide deprotection affords maleimido-oligonucleotides suitable for conjugation, as assessed by their reaction with different thiols.

Fluorescent ferritin nanoparticles and application to the aptamer sensor

We synthesized fluorescent ferritin nanoparticles (FFNPs) through bacterial expression of the hybrid gene consisting of human ferritin heavy chain (hFTN-H), spacer (glycine-rich peptide), and enhanced green (or red) fluorescent protein [eGFP (or DsRed)] genes. The self-assembly activity of hFTN-H that leads to the formation of nanoparticles (12 nm in diameter), the conformational flexibility of the C-terminus of hFTN-H, and the glycine-rich spacer enabled eGFPs (or DsReds) to be well displayed on the surface of each ferritin nanoparticle, resulting in the construction of green (or red) FFNPs [gFFNPs (or rFFNPs)]. As compared to eGFP (or DsRed) alone, it is notable that the developed FFNPs showed significantly amplified fluorescence intensity and also enhanced stability. DNA aptamers were chemically conjugated to gFFNP via each eGFP's cysteine residue that was newly introduced through site-directed mutagenesis (Ser175Cys). The DNA-aptamer-conjugated gFFNPs were used as a fluorescent reporter probe in the aptamer-based "sandwich" assay of a cancer marker [i.e., platelet-derived growth factor B-chain homodimer (PDGF-BB)] in phosphate-buffered saline buffer or diluted human serum. This is a simple two-step assay without any additional steps for signal amplification, showing that compared to the same aptamer-based assays using eGFP alone or Cy3, the detection signals, affinity of the reporter probe to the cancer marker, and assay sensitivity were significantly enhanced; i.e., the limit of detection was lowered to the 100 fM level. Although the PDGF-BB assay is reported here as a proof-of-concept, the developed FFNPs can be applied in general to any aptamer-based sandwich assays.

DNA-enzyme conjugate with a weak inhibitor that can specifically detect thrombin in a homogeneous medium

We present the DNA-assisted control of enzymatic activity for the detection of a target protein using a new type of DNA-enzyme conjugate. The conjugate is composed of an enzyme inhibitor to regulate enzyme activity and a DNA aptamer to be responsive toward the analyte protein. Glutathione S-transferase (GST) and thrombin were selected as a model enzyme and an analyte protein. A hexahistidine tag was genetically attached to the C terminus of the GST, and the 5' end of an oligonucleotide was conjugated with nitrilotriacetic acid (NTA) for the site-specific conjugation of the DNA with the GST based on a Ni(2+) complex interaction. We found that fluorescein acted as a weak inhibitor of GST and succeeded in the regulation of GST activity by increasing the local concentration of the weak inhibitor by the hybridization of a 3'-end fluorescein-modified DNA. The catalytic activity of the DNA aptamer-enzyme conjugate showed a dose-dependent response to thrombin, indicating that the GST activity was clearly recovered by the binding of the DNA aptamer to thrombin. The current system enables the sensitive and specific detection of thrombin simply by measuring the enzymatic activity in a homogeneous medium.

Controlled stoichiometric synthesis of DNA-quantum dot conjugates using Ni-mediated coordination chemistry

An oligonucleotide modified with Ni-nitrilotriacetate (NTA) was successfully synthesized and used for the stoichiometric functionalization of QDs. This synthetic approach allowed for the facile preparation of DNA-QD conjugates with a defined DNA/QD ratio using well-known Ni-histidine coordination chemistry. A FRET based DNA-QD nanoprobe was prepared using this method highlighting the great potential of this synthetic strategy.

Conjugation of fluorescent proteins with DNA oligonucleotides

This work describes the synthesis of covalent ssDNA conjugates of six fluorescent proteins, ECFP, EGFP, E(2)GFP, mDsRed, Dronpa, and mCherry, which were cloned with an accessible C-terminal cystein residue to enable site-selective coupling using a heterobispecific cross-linker. The resulting conjugates revealed similar fluorescence emission intensity to the unconjugated proteins, and the functionality of the tethered oligonucleotide was proven by specific Watson-Crick base pairing to cDNA-modified gold nanoparticles. Fluorescence spectroscopy analysis indicated that the fluorescence of the FP is quenched by the gold particle, and the extent of quenching varied with the intrinsic spectroscopic properties of FP as well as with the configuration of surface attachment. Since this study demonstrates that biological fluorophores can be selectively incorporated into and optically coupled with nanoparticle-based devices, applications in DNA-based nanofabrication can be foreseen.

Photoregulated assembly/disassembly of DNA-templated protein arrays using modified oligonucleotide carrying azobenzene side chains

DNA-templated self-assembly of nanomaterials provides great potential for applications including biosensors, nanoelectronics, and programmable and autonomous molecular machines. To switch or regulate the activities of those nanobiotechnological devices, non-invasive methods to assemble and disassemble specific nanoscale components are needed. Here, we describe photocontrol of assembly of DNA-templated protein arrays in solution, by using photo-controlled duplex formation of oligonucleotides carrying azobenzene. As a proof of concept prototype, we designed a one-dimensional protein array system that consists of a scaffold of DNA and two kinds of anchor DNA that were conjugated with fluorescent proteins (CFP and YFP, respectively). The scaffold DNA was modified to carry multiple azobenzene side chains so that the hybridization involving the scaffold DNA is regulated by photoirradiation through conformational changes of the azobenzene moieties. Melting temperatures of duplex made of the modified DNA scaffold and an anchor oligonucleotide were shifted significantly and reversibly by UV and visible photoirradiation (difference of T(m) was 34.8 degrees C in 150 mM potassium acetate). Measurements of Förster resonance energy transfer between CFP and YFP showed that the assembly of the protein array system was also changed by photoirradiation. Such non-invasive and reversible method to control assembly/disassembly of multiple, specific proteins in a DNA-templated protein array system would provide many functions for nanobiotechnological devices such as on/off switches and the ability to change the configuration reversibly.

Semisynthetic DNA-protein conjugates for biosensing and nanofabrication

Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.

Intracellular bioconjugation of targeted proteins with semiconductor quantum dots

We demonstrate controlled in vivo bioconjugation of a targeted intracellular protein to semiconductor quantum dots (QDs). Metal-affinity driven coordination of oligohistidine-appended proteins for chelated divalent cations was exploited to facilitate this interaction. Monomeric mCherry red fluorescent protein recombinantly engineered to express an N-terminal hexahistidine sequence was expressed from a eukaryotic plasmid vector following transfection into COS-1 cells. QDs solubilized with a carboxylated polymeric ligand and pretreated with Ni(2+) were then microinjected into the mCherry-expressing COS-1 cells. Förster resonance energy transfer (FRET) between the central QD donors and mCherry acceptors specifically coordinated to their surface was utilized to probe and confirm intracellular conjugate formation. We unexpectedly found that mCherry attachment to the QDs also substantially improves its resistance to photobleaching. This proof-of-concept, highlighting targeted intracellular bioconjugation to QDs, suggests that many cytoplasmic proteins expressing the ubiquitous hexahistidine affinity handle can be specifically attached to QDs in vivo. This approach can facilitate long-term monitoring of their spatio-temporal activity or, alternatively, allow engineering and in situ assembly of designer chimeric QD-fluorescent protein sensors.

N-linked glycosylation is essential for the stability but not the signaling function of the interleukin-6 signal transducer glycoprotein 130

N-Linked glycosylation is an important determinant of protein structure and function. The interleukin-6 signal transducer glycoprotein 130 (gp130) is a common co-receptor for cytokines of the interleukin (IL)-6 family and is N-glycosylated at 9 of 11 potential sites. Whereas N-glycosylation of the extracellular domains D1-D3 of gp130 has been shown to be dispensable for binding of the gp130 ligand IL-6 and its cognate receptor in vitro, the role of the N-linked glycans on domains D4 and D6 is still unclear. We have mutated the asparagines of all nine functional N-glycosylation sites of gp130 to glutamine and systematically analyzed the consequences of deleted N-glycosylation (dNG) in both cellular gp130 and in a soluble gp130-IgG1-Fc fusion protein (sgp130Fc). Our results show that sgp130Fc-dNG is inherently unstable and degrades rapidly under conditions that do not harm wild-type sgp130Fc. Consistently, the bulk of cellular gp130-dNG is not transported to the plasma membrane but is degraded in the proteasome. However, the small quantities of gp130-dNG, which do reach the cell surface, are still able to activate the key gp130 signaling target signal transducer and activator of transcription-3 (STAT3) upon binding of the agonistic complex of IL-6 and soluble IL-6 receptor. In conclusion, N-linked glycosylation is required for the stability but not the signal-transducing function of gp130.

Single-molecule investigations of a photoswitchable nanodevice

Due to the specificity of Watson-Crick base pairing, DNA is an excellent molecule for the fabrication of nanostructures. It has been shown that DNA can be used as a scaffold for positioning proteins and synthetic molecules with nanometer accuracy. As the next step in adding complexity and functionality to these nanodevices, optical addressability is incorporated. The fluorescent protein Dronpa, which can be optically switched between a fluorescent state and a dark state, is mounted on a DNA scaffold in the proximity of a synthetic fluorophore. Hence, the system can be optically switched between the dark state and an optically active state that undergoes Förster resonance energy transfer. As nanodevices operate as individual units, the functionality of the device is analyzed using single-molecule microscopy. The physical characteristics of nanodevices make them well suited as probes for investigating cellular processes or as shuttles for gene therapy. Hence, the functionality of the nanodevice is verified in the context of cellular measurements.

Apoenzyme reconstitution as a chemical tool for structural enzymology and biotechnology

Many enzymes contain a nondiffusible organic cofactor, often termed a prosthetic group, which is located in the active site and essential for the catalytic activity of the enzyme. These cofactors can often be extracted from the protein to yield the respective apoenzyme, which can subsequently be reconstituted with an artificial analogue of the native cofactor. Nowadays a large variety of synthetic cofactors can be used for the reconstitution of apoenzymes and, thus, generate novel semisynthetic enzymes. This approach has been refined over the past decades to become a versatile tool of structural enzymology to elucidate structure-function relationships of enzymes. Moreover, the reconstitution of apoenzymes can also be used to generate enzymes possessing enhanced or even entirely new functionality. This Review gives an overview on historical developments and the current state-of-the-art on apoenzyme reconstitution.

Design of DNA-conjugated polypeptide-based capture probes for the anchoring of proteins to DNA matrices

A new method for protein surface functionalization was developed that utilizes DNA-conjugated artificial polypeptides to capture recombinant target proteins from the solution phase and direct their deposition onto DNA-functionalized matrices. Protein capture is accomplished through the coiled-coil association of an engineered pair of heterodimeric leucine zippers. Incorporating half of the zipper complex directly into the polypeptides and labeling these polymers with ssDNA enables the polypeptide conjugates to form intermediate linkages that connect the target proteins securely to DNA-functionalized supports. This synthetic route provides an important alternative to conventional DNA-conjugation techniques by allowing proteins to be outfitted site-specifically with ssDNA while minimizing the need for postexpression processing. We demonstrate these attributes by (i) using the capture probes to prepare protein microarrays, (ii) demonstrating control over enzyme activity via deposition of DNA, and, (iii) synthesizing finite-sized, multiprotein complexes that are templated on designed DNA scaffolds in near quantitative yield.

Synthesis and Applications of Covalent Protein-DNA Conjugates

Synthetic protein-DNA conjugates are valuable tools with applications in fields including nanobiotechnology, bioanalytical chemistry, and molecular diagnostics, and various synthetic methods for their production have been developed during the past three decades. The present article reviews current methodologies for the synthesis of covalent protein-DNA conjugates with particular focus on the regiospecificity and stoichiometry of these reactions.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Self-assembled donor comprising quantum dots and fluorescent proteins for long-range fluorescence resonance energy transfer

We report on the development of a self-assembled donor for long-range fluorescence resonance energy transfer (FRET). To this end, a three-chromophore FRET (3Ch-FRET) system was constructed, which consists of a luminescent quantum dot (QD), enhanced yellow fluorescent proteins (EYFP), and Atto647-dye-modified oligonucleotides. The system was assembled by electrostatic binding of covalent EYFP-ssDNA conjugate to the QD and subsequent hybridization with complementary oligonucleotides labeled with Atto647-dye. The final conjugates comprise three different two-chromophore FRET (2Ch-FRET) subsystems, QD/EYFP, QD/Atto647, and EYFP/Atto647, respectively, which were studied in detail by steady-state and time-resolved photoluminescence measurements. The helicity of DNA allowed us to control donor/acceptor separations and thus enabled the detailed analysis of the various FRET processes. We found that the 2Ch-FRET and the 3Ch-FRET (QD/EYFP/Atto647) systems revealed FRET efficiencies and transfer rates that were affected by the availability of distinct FRET pathways. The derived energy-transfer efficiencies and Förster radii indicated that within the 3Ch-FRET system, the 2Ch-FRET subsystem QD/EYFP showed highest FRET efficiencies ranging from 64 to 72%. Thus, it can be used as a powerful donor system that combines the intrinsic advantages of QDs (large and spectrally broad absorption cross section) and EYFP (high quantum yield) and enables long-distance FRET processes for donor-acceptor distances of up to 13 nm.

Self-Directed and Self-Oriented Immobilization of Antibody by Protein G−DNA Conjugate

A versatile biolinker for efficient antibody immobilization was prepared by site-specific coupling of protein G to DNA oligonucleotide. This protein G-DNA conjugate ensures the controlled immobilization of an antibody to the intended area on the surface of bioassay chips or particles, while maintaining the activity and orientation of the bound antibody. Streptococcus protein G tagged with a cysteine residue at the N-terminus was chemically linked to amine-modified, single-stranded DNA. SPR analysis indicated that the protein G-DNA conjugates sequence-specifically bind to complementary surface-bound DNA probes. More importantly, the resulting protein G, which is hybridized onto the DNA surface, possesses a greater antibody/antigen binding ability than even properly oriented protein G linked on the chip surface by chemical bonding. Antibody targeting on glass slides could also be achieved by using this linker system without modifying or spotting antibodies. Moreover, the protein G-DNA conjugate provided a simple but effective method to label DNA-functionalized gold nanoparticles with target antibodies. The DNA-linked protein G construct introduced in this study offers a useful strategy to manage antibody immobilization in many immunoassay systems.

Microtiter plate-based screening for the optimization of DNA-protein conjugate synthesis by means of expressed protein ligation

We report a rapid microtiter plate screening assay for the optimization of the synthesis of covalent DNA-protein conjugates by means of expressed protein ligation (EPL). The EPL method allows for the site-specific coupling of cysteine-modified DNA oligomers with recombinant intein-fusion proteins, the latter containing a C-terminal thioester that enables a mild and highly specific reaction with N-terminal cysteine compounds. To screen for optimal reaction conditions, we developed a microtiter plate-based assay that utilizes DNA-directed immobilization of the products formed in the ligation reaction of cysteine-modified DNA oligonucleotides with the model protein thioester of the maltose-binding protein (MBP), recombinantly expressed as an intein-fusion protein in E. coli. The screening assay allowed the rapid quantitative monitoring of various reaction parameters, such as the ratio of the reactants, reaction times, pH and ion strength of the buffer, the influence of various thiol additives and the nature of the chemical linker within the cysteine-bearing DNA oligonucleotide. As the consequence of the assay-based optimization, the ligation of MBP with the oligonucleotide was improved to near quantitative yields.