Methyltransferase-directed covalent coupling of fluorophores to DNA

Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a global presence in healthcare facilities as well as community settings. The resistance of MRSA to beta-lactam antibiotics can be attributed to a mobile genetic element called the staphylococcal cassette chromosome mec (SCCmec), ranging from 23 to 68 kilobase pairs in length. The mec gene complex contained in SCCmec allows MRSA to survive in the presence of penicillin and other beta-lactam antibiotics. We demonstrate that optical mapping (OM) is able to identify the bacterium as S. aureus, followed by an investigation of the presence of kilobase pair range SCCmec elements by examining the associated OM-generated barcode patterns. By employing OM as an alternative to traditional DNA sequencing, we showcase its potential for the detection of complex genetic elements such as SCCmec in MRSA. This approach holds promise for enhancing our understanding of antibiotic resistance mechanisms and facilitating the development of targeted interventions against MRSA infections.

A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells

Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.

Reactive Phenanthrene Derivatives as Markers of Amino Groups in Fluorescence Microscopy of Surface Modified Micro-Zeolite L

Two reactive phenanthrene derivatives, 4-(1H phenanthrol [9,10-d] imidazole-2-yl) benzaldehyde (PIB) and 6,9-dimethoxyphenanthro[9,10-c]furan-1,3-dione (PA) with high fluorescent quantum yields were prepared and used as fluorescent marker in fluorescence microscopy. In particular, silane modified μmZeolite-L containing amino group (-NH₂) in the surface were labeled with the phenanthrene derivatives allowing good imaging resolution and spectroscopy measurements. The presence of a large Stokes shift of the probes due to their intramolecular charge-transfer character gives an advantage of the compounds in confocal laser fluorescence microscopy due to easy signal separation in excitation and emission wavelengths. On the other hand, these results open up the possibility of using these probes for visualization of Zeolite-based materials commonly used as catalysts in thermal and photochemical reactions.

Harnessing methylation and AdoMet-utilising enzymes for selective modification in cascade reactions

Enzyme-mediated methylation is a very important reaction in nature, yielding a wide range of modified natural products, diversifying small molecules and fine-tuning the activity of biomacromolecules. The field has attracted much attention over the recent years and interesting applications of the dedicated enzymes in biocatalysis and biomolecular labelling have emerged. In this review article, we summarise the concepts and recent advances in developing (chemo)-enzymatic cascades for selective methylation, alkylation and photocaging as tools to study biological methylation and as biotransformations to generate site-specifically alkylated products.

Enzyme-mediated bioorthogonal technologies: catalysts, chemoselective reactions and recent methyltransferase applications

Transferases have emerged as among the best catalysts for enzyme-mediated bioorthogonal functional group installation to advance innovative in vitro, cell-based and in vivo chemical biology applications. This review introduces the key considerations for selecting enzyme catalysts and chemoselective reactions most amenable to bioorthogonal platform development and highlights relevant key technology development and applications for one ubiquitous transferase subclass - methyltransferases (MTs). Within this context, recent advances in MT-enabled bioorthogonal labeling/conjugation relevant to DNA, RNA, protein, and natural products (i.e. complex small molecule metabolites) are highlighted.

FRET-Based Method for Direct, Real-Time Measurement of DNA Methyltransferase Activity

DNA methyltransferase activity is associated with a host of diseases, including cancers, where global hypomethylation of the genome, as well as marked changes in local DNA methylation patterns, can be both diagnostic and prognostic for the disease. Despite this, we currently lack a method for directly measuring the activity of the DNA methyltransferases, which would support the development of DNA methyltransferase-targeted therapies. Here, we demonstrate an assay for the direct measurement of methyltransferase activity, in real time. We employ a fluorescent methyltransferase cofactor analogue, which when bound by the enzyme to a labeled target DNA sequence results in fluorescence resonance energy transfer (FRET) between the donor dye (DNA) and the acceptor dye (cofactor). We demonstrate that the method can be used to monitor the activity of DNA MTases in real time and can be applied to screen inhibitors of the DNA methyltransferases. We show this in both bulk phase and single molecule imaging experiments, highlighting the potential application of the assay in screening and biophysical studies of methyltransferase function.

Covalent labeling of nucleic acids

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.

Label as you fold: methyltransferase-assisted functionalization of DNA nanostructures

Non-DNA labels are key components for the construction of functional DNA nanostructures. Here, we present a method to graft covalent labels onto DNA origami nanostructures in an enzymatic one-pot reaction. The DNA methyltransferase M.TaqI labels the DNA nanostructures with azide groups, which serve as universal attachment points via click chemistry. Direct labeling with fluorescent dyes is also demonstrated. The procedure yields structures with high fluorescence intensities and narrow intensity distributions. In combination with UV crosslinking it enables the creation of temperature-stable, intense fluorescent beacons.

Site-Selective and Rewritable Labeling of DNA through Enzymatic, Reversible, and Click Chemistries

Current methods for bioconjugation rely on the introduction of stable linkers that lack the required versatility to perform sequential functionalizations. However, sequential manipulations are an increasing requirement in chemical biology because they can underpin multiple analyses of the same sample to provide a wider understanding of cell behavior. Here, we present a new method to site-selectively write, remove, and rewrite chemical functionality to a biomolecule, DNA in this case. Our method combines the precision and robustness of methyltransferase-directed labeling with the reversibility of acyl hydrazones and the efficiency of click chemistry. Underpinning the method is a new S-adenosyl-l-methionine derivative to site-selectively label DNA with a bifunctional chemical handle containing an acyl hydrazone-linker and a terminal azide. Functional tags are conjugated via the azide and can be removed (i.e., untagged) when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either rewritten to reset the original chemical handle or covalently reacted with a permanent tag. This ability to write, tag, untag, and permanently tag DNA is exploited to sequentially introduce two fluorescent dyes on DNA. Finally, we demonstrate the potential of the method by developing a protocol to sort labeled DNA using magnetic beads, with subsequent amplification of the sorted DNA sample for further analysis. The presented method opens new avenues for site-selective bioconjugation and should underpin integrative approaches in chemical biology where sequential functionalizations of the same sample are required.

DNA barcodes for rapid, whole genome, single-molecule analyses

We report an approach for visualizing DNA sequence and using these ‘DNA barcodes’ to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.

Fluorescent SAM analogues for methyltransferase based DNA labeling

In this work, the preparation of new S-adenosyl-l-methionine (SAM) analogues for sequence specific DNA labeling is evaluated. Fluorescent cofactors were synthesized and their applicability in methyltransferase based optical mapping is demonstrated.

One-step microchip for DNA fluorescent labeling

In this study, we propose a microchip that is sequentially capable of fluorescently staining and washing DNAs. The main advantage of this microchip is that it allows for one-step preparation of small amounts of solution without degrading microscopic bio-objects such as the DNAs, cells, and biomolecules to be stained. The microchip consists of two inlets, the main channel, staining zone, washing zone, and one outlet, and was processed using a femtosecond laser system. High molecular transport of rhodamine B to deionized water was observed in the performance test of the microchip. Results revealed that the one-step procedure of on-chip DNA staining and washing was excellent compared to the conventional staining method. The one-step preparation of stained and washed DNAs through the microchip will be useful for preparing small volumes of experimental samples.

Click-Type Protein-DNA Conjugation for Mn2+ Imaging in Living Cells

A click-type protein-DNA conjugation, named as MnDDC (Mn²⁺-activated DCV-DNA conjunction), is presented, where DCV (rep protein of duck circovirus) and its target DNA work as the modular blocks to rapidly and effectively generate Mn²⁺-dependent and site-specific protein-DNA linkage. On the basis of MnDCC, a fluorescent Mn²⁺ biosensor composed of DCV and a molecular beacon, was developed for rapid sensing of Mn²⁺ within 2 min with nanomolar sensitivity. Using the proposed biosensor, not only analysis of Mn²⁺ in real samples (e.g., serum and food), but also wash-free fluorescent imaging of Mn²⁺ in extracellular environment and cytoplasm have been achieved. Moreover, the MnDDC-based sensor was proved to be a powerful tool for visualization of Mn²⁺ during exploration of the associated cytotoxicity in living neural cells, which is helpful to reveal the cellular responses toward the disordered homeostasis of Mn²⁺ in both extracellular and intracellular microenvironments.

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

Electric Single-Molecule Hybridization Detector for Short DNA Fragments

By combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipets, we demonstrate an electric, label-free hybridization sensor for short DNA sequences (<100 nucleotides). Such short fragments are known to occur as circulating cell-free DNA in various bodily fluids, such as blood plasma and saliva, and have been identified as disease markers for cancer and infectious diseases. To this end, we use as a model system an 88-mer target from the RV1910c gene in Mycobacterium tuberculosis, which is associated with antibiotic (isoniazid) resistance in TB. Upon binding to short probes attached to long carrier DNA, we show that resistive-pulse sensing in nanopipets is capable of identifying rather subtle structural differences, such as the hybridization state of the probes, in a statistically robust manner. With significant potential toward multiplexing and high-throughput analysis, our study points toward a new, single-molecule DNA-assay technology that is fast, easy to use, and compatible with point-of-care environments.

Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA

Produced as linear biopolymers from four major types of building blocks, DNA and RNA are further furnished with a range of covalent modifications. Despite the impressive specificity of natural enzymes, the transferred groups are often poor reporters and not amenable to further derivatization. Therefore, strategies based on repurposing some of these enzymatic reactions to accept derivatized versions of the transferrable groups have been exploited. By far the most widely used are S-adenosylmethionine-dependent methyltransferases, which along with several other nucleic acids modifying enzymes offer a broad selection of tagging chemistries and molecular features on DNA and RNA that can be targeted in vitro and in vivo. Engineered enzymatic reactions have been implemented in validated DNA sequencing-based protocols for epigenome analysis. The utility of chemo-enzymatic labeling is further enhanced with recent advances in physical detection of individual reporter groups on DNA using super resolution microscopy and nanopore sensing enabling single-molecule multiplex analysis of genetic and epigenetic marks in minute samples. Altogether, a number of new powerful techniques are currently in use or on the verge of real benchtop applications as research tools or next generation diagnostics.

DNA-Functionalized Dye-Loaded Polymeric Nanoparticles: Ultrabright FRET Platform for Amplified Detection of Nucleic Acids

Going beyond the limits of optical biosensing motivates exploration of signal amplification strategies that convert a single molecular recognition event into a response equivalent to hundreds of fluorescent dyes. In this respect, Førster Resonance Energy Transfer (FRET) with bright fluorescent nanoparticles (NPs) is an attractive direction, but it is limited by poor efficiency of NPs as FRET donors, because their size is typically much larger than the Førster radius (∼5 nm). Here, we established FRET-based nanoparticle probes that overcome this fundamental limitation by exploiting a phenomenon of giant light harvesting with thousands of strongly coupled dyes in a polymer matrix. These nanoprobes are based on 40 nm dye-loaded poly(methyl methacrylate- co-methacrylic acid) (PMMA-MA) NPs, so-called light-harvesting nanoantennas, which are functionalized at their surface with oligonucleotides. To achieve this functionalization, we developed an original methodology: PMMA-MA was modified with azide/carboxylate bifunctional group that enabled assembly of small polymeric NPs and their further Cu-free click coupling with oligonucleotides. The obtained functionalized nanoantenna behaves as giant energy donor, where hybridization of target nucleic acid (encoding survivin cancer marker) with ∼23 grafted oligonucleotides/Cy5-acceptors switches on/off FRET from ∼3200 rhodamine-donors of the nanoantenna, leading to 75-fold signal amplification. In solution and on surfaces at single-particle level, the nanoprobe provides sequence-specific two-color ratiometric response to nucleic acids with limit of detection reaching 0.25 pM. It displays unprecedented brightness for a FRET biosensor: it outperforms analogous FRET-based molecular probe by >2000-fold and QDot-605 by ∼100-fold. The developed concept of amplified sensing will increase orders of magnitude sensitivity of fluorescent probes for biomolecular targets.