Fluorescence-labeled DNA Research Articles

Pressure-driven formation of sub-femtoliter droplets in constricted T-shaped nanofluidic channel and application to isolation and counting of single nanoparticles

Nanofluidics has developed, enabling the analysis of single nanoparticles such as viruses and macromolecules using nanochannels. However, since nanoparticles migrate randomly by Brownian motion with displacements comparable to the nanochannel size, it is difficult to array and process nanoparticles individually in continuous phase flows with biological analyte concentrations of pM–nM. The present study developed a method to generate aqueous droplets of 102 aL–100 fL volumes in an organic phase in a nanochannel by pressure-driven flow control, and applied the method to the isolation of single nanoparticles with 101−102 pM concentrations. A T-shaped nanochannel with a narrow constriction section was proposed to locally enhance the shear force to form smaller droplets by 102 kPa external pressure, without increasing the pressure loss by downscaling the channel. The proposed channel design was validated, droplets with 0.8–1.0 fL volumes were formed with pL/min flow rates at Ca = 0.5–1.4 × 10−3, and the dynamics of droplet generation was well characterized by the linear scaling law. Using the developed device, encapsulation and counting of single fluorescent nanoparticles and single fluorescently-labeled DNA molecules in droplets were successfully demonstrated. This work will contribute to the development of droplet nanofluidics and ultrasmall analytical applications.

Cyclopropenes as Chemical Reporters for Dual Bioorthogonal and Orthogonal Metabolic Labeling of DNA.

Dual bioorthogonal labeling enables the investigation and understanding of interactions in the biological environment that are not accessible by a single label. However, applying two bioorthogonal reactions in the same environment remains challenging due to cross-reactivity. We developed a pair of differently modified 2'-deoxynucleosides that solved this issue for dual and orthogonal labeling of DNA. Inverse-electron demand Diels-Alder and photoclick reactions were combined to attach two different fluorogenic labels to genomic DNA in cells. Using a small synthetic library of 1- and 3-methylcyclopropenyl-modified 2'-deoxynucleosides, two 2'-deoxyuridines were identified to be the fastest-reacting ones for each of the two bioorthogonal reactions. Their orthogonal reactivity could be evidenced in vitro. Primer extension experiments were performed with both 2'-deoxyuridines investigating their replication properties as substitutes for thymidine and evaluating subsequent labeling reactions on the DNA level. Finally, dual, orthogonal and metabolic fluorescent labeling of genomic DNA was demonstrated in HeLa cells. An experimental procedure was developed combining intracellular transport and metabolic DNA incorporation of the two 2'-deoxyuridines with the subsequent dual bioorthogonal labeling using a fluorogenic cyanine-styryl tetrazine and a fluorogenic pyrene-tetrazole. These results are fundamental for advanced metabolic labeling strategies for nucleic acids in the future, especially for live cell experiments.

Cyclopropene als Chemische Reporter für die Duale Bioorthogonale und Orthogonale Metabolische Markierung von DNA

AbstractDie duale bioorthogonale Markierung ermöglicht die Untersuchung und das Verständnis von Wechselwirkungen in der biologischen Umgebung, die mit einer einzigen Markierung nicht zugänglich sind. Eine Herausforderung bleibt jedoch die Anwendung von zwei bioorthogonalen Reaktionen in der gleichen Umgebung aufgrund von Kreuzreaktivität. Um dieses Problem für die duale und orthogonale Markierung von DNA zu lösen, haben wir zwei unterschiedlich modifizierte 2′‐Desoxynukleoside entwickelt. Mit Hilfe der Diels‐Alder‐Reaktion mit inversem Elektronenbedarf und Photoklick‐Reaktion wurde genomische DNA in Zellen mit zwei verschiedenen fluorogenen Markern verknüpft. Aus einer kleinen synthetischen Bibliothek aus 1‐ und 3‐methylcyclopropenyl‐modifizierten 2′‐Desoxynukleosiden wurden zwei 2′‐Desoxyuridine identifiziert, die am schnellsten in jeweils einer der beiden bioorthogonalen Reaktionen reagieren. Ihre orthogonale Reaktivität konnte in vitro nachgewiesen werden. Ihre Replikationseigenschaften als Ersatz für Thymidin wurden in Primerverlängerungsexperimenten untersucht, um die anschließenden Markierungsreaktionen an DNA abzuschätzen. Schließlich wurde eine duale, orthogonale und metabolische Fluoreszenzmarkierung von genomischer DNA in HeLa‐Zellen nachgewiesen. Es wurde ein experimentelles Protokoll entwickelt, das den intrazellulären Transport und den metabolischen DNA‐Einbau der beiden 2′‐Desoxyuridine mit der anschließenden dualen bioorthogonalen Markierung unter Verwendung eines fluorogenen Cyanin‐Styryl‐Tetrazins und eines fluorogenen Pyren‐Tetrazols kombiniert. Diese Ergebnisse sind von grundlegender Bedeutung für fortgeschrittene metabolische Markierungsstrategien für Nukleinsäuren in der Zukunft, insbesondere in lebenden Zellen.

MiR-21 Responsive Nanocarrier Targeting Ovarian Cancer Cells

In recent years, DNA origami-based nanocarriers have been extensively utilized for efficient cancer therapy. However, developing a nanocarrier capable of effectively protecting cargos such as RNA remains a challenge. In this study, we designed a compact and controllable DNA tubular origami (DTO) measuring 120 nm in length and 18 nm in width. The DTO exhibited appropriate structural characteristics for encapsulating and safeguarding cargo. Inside the DTO, we incorporated 20 connecting points to facilitate the delivery of cargoes to various ovarian and normal epithelial cell lines. Specifically, fluorescent-labeled DNA strands were attached to these sites as cargoes. The DTO was engineered to open upon encountering miR-21 through RNA/DNA strand displacement. Significantly, for the first time, we inhibited fluorescence using the compact DNA nanotube and observed dynamic fluorescent signals, indicating the controllable opening of DTO through live-cell imaging. Our results demonstrated that the DTO remained properly closed, exhibited effective internalization in ovarian cancer cells in vitro, showcasing marked differential expression of miR-21, and efficiently opened with short-term exposure to miR-21. Leveraging its autonomous behavior and compact design, the DTO emerges as a promising nanocarrier for various clinically relevant materials. It holds significant application prospects in anti-cancer therapy and the development of flexible biosensors.

Determining the Compaction State of Genes Using DNA FISH.

DNA fluorescence in situ hybridization (FISH) enables the visualization of chromatin architecture and the interactions between genomic loci at a single-cell level, complementary to genome-wide methods such as Hi-C. DNA FISH uses fluorescent-labeled DNA probes targeted to the loci of interest, allowing for the analysis of their spatial positioning and proximity with microscopy. Here, we describe an optimized experimental procedure for DNA FISH, from probe design and sample preparation through imaging and image quantification. This protocol can be readily applied to querying the spatial positioning of genomic loci of interest.

Microarray biochip fabricated on silicon nanowires/carbon dots heterostructures for enhanced viral DNA detection

Recent studies have shown that human oncoviruses are responsible for 10% of cancer cases worldwide. While PCR assays are highly sensitive and specific, microarrays offer outstanding performance for detecting multiple targets simultaneously. However, in microarray systems, accurate detection of DNA viruses relies on the type of microarray platform, while obtaining high-quality, fluorescent-labelled single-stranded DNA bares an equal contribution.Our study demonstrates a proof-of-concept of a microarray platform for enhanced DNA detection. First, we assembled 3D microarray chips on silicon nanowires (SiNWs) substrates using a one-step metal-assisted chemical etching (1-MACE) technique, coated them with SU-8 polymer, and ornated with carbon quantum dots (CDs) in either poly(diallyldimethylammonium) PDDA or poly(ethyleneimine) PEI solutions. Second, we obtained high-quality labelled HPV 16 target ssDNA through classic PCR and asymmetric PCR with a nested primer labelled with Cy5, then hybridised the ssDNA on the SiNWs/SU-8/CDs platforms.The fluorescent signal of hybridised DNA was strongest on the SiNWs/SU-8 substrates, and adding CDs further enhanced the signal. The best signal intensities (4.303, 3.7) and coefficients of variation (3.12%, 2.59%) were achieved by combining HPV 16 probes co-immobilised with CDs functionalised with PDDA. Our study conclusively demonstrates the vast potential of this microarray platform for improved DNA detection.

Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry.

We have devised a single pot, low-cost method to add azide groups to unmodified nucleic acids without the need for enzymes or chemically modified nucleoside triphosphates. This involves reacting an azide-containing sulfinate salt with the nucleic acid, leading to replacement of C-H bonds on the nucleobase aromatic rings with C-R, where R is the azide-containing linker derived from the original sulfinate salt. With the addition of azide functional groups, the modified nucleic acid can easily be reacted with any alkyne-labeled compound of interest, including fluorescent dyes as shown in this work. This methodology enables the fluorescent labeling of a wide variety of nucleic acids, including natively folded RNAs, under mild conditions with minimal effects upon biochemical function and ribozyme catalysis. To demonstrate this, we show that a pair of labeled complementary ssDNA oligonucleotides (oligos) can hybridize to form dsDNA, even when labeled with multiple fluorophores per oligo. In addition, we also demonstrate that two different group II introns can splice when prelabeled internally with fluorophores, using our method. Broadly, this demonstrates that sulfinate modification of RNA is compatible with ribozyme function and Watson-Crick pairing, while preserving the labile backbone.

Rapid, inexpensive, sequence-independent fluorescent labeling of phosphorothioate DNA

Fluorescently labeled oligonucleotides are powerful tools for characterizing DNA processes; however, their use is limited by the cost and sequence requirements of current labeling technologies. Here, we develop an easy, inexpensive, and sequence-independent method for site-specifically labeling DNA oligonucleotides. We utilize commercially synthesized oligonucleotides containing phosphorothioate diester(s) in which a nonbridging oxygen is replaced with a sulfur (PS-DNA). The increased nucleophilicity of the thiophosphoryl sulfur relative to the phosphoryl oxygen permits selective reactivity with iodoacetamide compounds. As such, we leverage a long-existing bifunctional linker, N,N′-bis(α-iodoacetyl)-2-2′-dithiobis(ethylamine) (BIDBE), that reacts with PS-DNAs to leave a free thiol, allowing conjugation of the wide variety of commercial maleimide-functionalized compounds. We optimized BIDBE synthesis and its attachment to PS-DNA and then fluorescently labeled the BIDBE-PS-DNA using standard protocols for labeling cysteines. We purified the individual epimers, and using single-molecule Förster resonance energy transfer (FRET), we show that the FRET efficiency is independent of the epimeric attachment. Subsequently, we demonstrate that an epimeric mixture of double-labeled Holliday junctions (HJs) can be used to characterize their conformational properties in the absence and presence of the structure-specific endonuclease Drosophila melanogaster Gen. Finally, we use a biochemical activity assay to show that this double-labeled HJ is functional for cleavage by Gen and that the double-labeled HJ allows multiple DNA species to be identified in a single experiment. In conclusion, our results indicate that dye-labeled BIDBE-PS-DNAs are comparable to commercially labeled DNAs at a significantly reduced cost. Notably, this technology could be applied to other maleimide-functionalized compounds, such as spin labels, biotin, and proteins. The sequence independence of labeling, coupled with its ease and low cost, enables unrestricted exploration of dye placement and choice, providing the potential for creation of differentially labeled DNA libraries and opening previously inaccessible experimental avenues.

A novel proteinaceous molecule produced by Lysinibacillus sp. OF-1 depends on the Ami oligopeptide transporter to kill Streptococcus pneumoniae.

Infections caused by antibiotic-resistant Streptococcus pneumoniae are of growing concern for healthcare systems, which need new treatment options. Screening microorganisms in terrestrial environments has proved successful for discovering antibiotics, while production of antimicrobials by marine microorganisms remains underexplored. Here we have screened microorganisms sampled from the Oslo Fjord in Norway for production of molecules that prevent the human pathogen S. pneumoniae from growing. A bacterium belonging to the genus Lysinibacillus was identified. We show that this bacterium produces a molecule that kills a wide range of streptococcal species. Genome mining in BAGEL4 and AntiSmash suggested that it was a new antimicrobial compound, and we therefore named it lysinicin OF. The compound was resistant to heat (100 °C) and polymyxin acylase but susceptible to proteinase K, showing that it is of proteinaceous nature, but most probably not a lipopeptide. S. pneumoniae became resistant to lysinicin OF by obtaining suppressor mutations in the ami locus, which encodes the AmiACDEF oligo peptide transporter. We created ΔamiC and ΔamiEF mutants to show that pneumococci expressing a compromised Ami system were resistant to lysinicin OF. Furthermore, by creating mutants expressing an intact but inactive Ami system (AmiED184A and AmiFD175A) we could conclude that the lysinicin OF activity depended on the active form (ATP-hydrolysing) of the Ami system. Microscopic imaging and fluorescent labelling of DNA showed that S. pneumoniae treated with lysinicin OF had an average reduced cell size with condensed DNA nucleoid, while the integrity of the cell membrane remained intact. The characteristics and possible mode of action of lysinicin OF are discussed.

Co-infecting phages impede each other's entry into the cell.

Bacteriophage lambda decides whether to pursue the lysogenic pathway based on the number of phages co-infecting the cell (multiplicity of infection, MOI). This strategy is believed to be a way for phages to infer the abundance of available bacterial hosts. However, the single-cell assessment would reliably reflect the environment only if the intracellular number of phages is proportional to the extracellular ratio of phages to bacteria. It is unknown whether this premise is true. Here, we show that co-infecting phages impede each other's entry into the cell, thus reducing the effective MOI that drives the decision. Using fluorescent labeling of phage capsids and DNA, we found that the intracellular number of phage genomes scales sublinearly with the number of phages adsorbed to the cell. Time-lapse measurements and mathematical modeling revealed that the entry probability per phage decreases with MOI, suggesting mutual interference between co-infecting phages at the entry stage. This effect likely reflects the phage-induced perturbations to the envelope integrity, ionic concentrations in the cytoplasm, and membrane potential of the infected cell. Since these perturbations are known to be MOI dependent, we reasoned that, the more phages infect the same cell, the more impeded their entries are. The degree to which phage entry is impeded successfully accounts for the different lysogenization frequencies measured in different infection media and recapitulates the heterogeneity in infection outcomes observed in individual cells. Altogether, our findings demonstrate the role played by entry dynamics in driving cell fate choice following lambda infection.

Super-resolution paint imaging with molecular beacon.

DNA-PAINT offers simple super-resolution imaging through the transient binding of fluorescently-labelled DNA imagers to target molecules. It has many advantages, including super-multiplexing capability and robustness against photobleaching. However, the unbound fluorescent imagers in the solution can cause high fluorescence background and place constraints on the imaging conditions that limit the technique's potential, such as low imager concentration, thin TIRF illumination, and long exposure time. In this study, we developed a new strategy to improve PAINT imaging using a fluorogenic molecular beacon (MB) as the imager. MB-PAINT eliminates false localizations from nonspecific surface adsorption and fluorescence background at concentrations far exceeding conventional linear imagers. Furthermore, MB-PAINT achieves similar nanometer localization precision to conventional DNA-PAINT. Lastly, we demonstrate that MB-PAINT is ideally suited for super-resolution tension imaging in living cells even at high frame rates, suppressing the potential of artifacts from free-diffusing and spontaneous binding of imagers at the cell-substrate interface.

Role of DNA sliding friction and nonequilibrium dynamics in viral DNA ejection and packaging.

In many viruses DNA is packaged to high densities, resulting in high “internal force” inside the capsid shell. This helps drive DNA ejection through the portal channel when viruses infect cells. Imaging of the in vitro ejection of fluorescent-labeled DNA from phages T5 and lambda found that it was initially slow despite the internal force being highest when the capsid is full. This was attributed to hydrodynamic drag on the tightly-packed DNA, but this hypothesis has not been tested. Here we introduce a new method for probing the DNA mobility by using optical tweezers to pull it out from phage phi29 capsids. This allows us to measure the dynamics with higher precision, avoid using DNA-binding dyes that alter the dynamics, and apply variable forces. We measure even slower DNA exit than reported previously, a steeper, exponential velocity increase as the first 20% of the genome length exits, and find that exit velocity is not proportional to driving force as expected for hydrodynamic friction. Rather, our findings are consistent with theoretical predictions for DNA-DNA sliding friction. We also observe large heterogeneity in the exit dynamics and stochastic pausing, indicating that ejection is a nonequilibrium process, in qualitative agreement with simulations. Features of the pausing suggest it is related to the phenomenon of “clogging” in soft-matter physics, which occurs in the flow of disordered materials through constrictions. Our results indicate that intramolecular friction and nonequilibrium pausing control the kinetics of ejection but that this friction does not significantly affect DNA packaging.

Dynamic concatenation leads to anomalous transport of ring DNA in concentrated solutions.

Circular DNA polymers have been widely studied due to their biological relevance as well as the unique anomalous transport properties they exhibit in concentrated solutions and blends with linear DNA. In cells, topoisomerase II relaxes torsional strain in circular DNA by cutting and then reconnecting one of the strands of the double-stranded polymer, enabling replication, transcription, and repair. When topoisomerase II acts on nicked circular DNA at high concentration, the relaxed rings can concatenate, forming Olympic ring structures reminiscent of kinetoplasts. The rate of topoisomerase activity as well as the concentration and size of the DNA can tune the nonequilibrium dynamics and conformations of the concatemers. Here, we visualize the fluorescent-labeled DNA rings comprising the concatemers and use particle tracking and differential dynamic microscopy to characterize the dynamics and time-varying size and shape of the actively linking and unlinking molecules. Beyond the insight our work provides to biological processes mediated by active restructuring of DNA, the complex fluids we engineer and study may have applications in the design of biocompatible active materials for cellular repair, toxin filtration and drug delivery.

Super-Resolution Tension PAINT Imaging with a Molecular Beacon.

DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.

The Use of Primers Heavily Labeled with Fluorescein in Polymerase Chain Reaction

The fluorescently-labeled DNA is widely used in various bioanalytical applications. For a number of applications, a high level of labeling could be beneficial. One of the ways to produce DNA fragments bearing multiple fluorescent tags is to use polymerase chain reaction (PCR) with primers heavily labeled with fluorophores. Here we tested how primers with multiple fluorescein tags perform in PCR. It has been found that the positioning of fluorescein tags at or near the 3'-end upon primer multiple labeling can inhibit DNA amplification (up to a complete stop when tags are placed at the 3'- or adjacent nucleotide). The mechanism, by which the presence of fluorescein tags at or near the primer 3'-end affects the PCR performance, is rather ambiguous and can involve both a steric hindrance for polymerase binding from the fluorescein moiety, as well as destabilization of a primer-template duplex. Nonetheless, if multiple fluorescein tags are attached so that at least three nucleotides from the primer 3'-end are unmodified, the production of DNA fragments bearing multiple fluorescein molecules is possible even if both primers are heavily labeled, though on the expense of amplicon yield.

Nanomaterials enabled and enhanced DNA-based biosensors.

DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.

Self-Supplying Guide RNA-Mediated CRISPR/Cas12a Fluorescence System for Sensitive Detection of T4 PNKP.

Sensitive detection methods for T4 polynucleotide kinase/phosphatase (T4 PNKPP) are urgently required to obtain information on malignancy and thereby to provide better guidance in PNKP-related diagnostics and drug screening. Although the CRISPR/Cas12a system shows great promise in DNA-based signal amplification protocols, its guide RNAs with small molecular weight often suffer nuclease degradation during storage and utilization, resulting in reduced activation efficiency. Herein, we proposed a self-supplying guide RNA-mediated CRISPR/Cas12a system for the sensitive detection of T4 PNKP in cancer cells, in which multiple copies of guide RNA were generated by in situ transcription. In this assay, T4 PNKP was chosen as a model, and a dsDNA probe with T7 promoter region and the transcription region of guide RNA were involved. Under the action of T4 PNKP, the 5'-hydroxyl group of the dsDNA probe was converted to a phosphate group, which can be recognized and digested by Lambda Exo, resulting in dsDNA hydrolysis. The transcription template was destroyed, which resulted in the failure to generate guide RNA by the transcription pathway. Therefore, the CRISPR/Cas12a system could not be activated to effectively cleavage the F-Q-reporter, and the fluorescence signal was turned off. In the absence of T4 PNKP, the 5'-hydroxyl group of the substrate DNA cannot be digested by Lambda Exo. The intact dsDNA acts as the transcription template to generate a large amount of guide RNA. Finally, the formed Cas12a/gRNA complex triggered the reverse cleavage of Cas12a on the F-Q-reporter, resulting in a "turn-on" fluorescence signal. This strategy displayed sharp sensitivity of T4 PNKP with the limit of detection (LOD) down to 0.0017 mU/mL, which was mainly due to the multiple regulation effect of transcription amplification. In our system, the dsDNA simultaneously serves as the T4 PNKP substrate, transcription template, and Lambda Exo substrate, avoiding the need for multiple probe designs and saving costs. By integrating the target recognition, Lambda Exo activity, and trans-cleavage activity of Cas12a, CRISPR/Cas12a catalyzed the cleavage of fluorescent-labeled short-stranded DNA probes and enabled synergetic signal amplification for sensitive T4 PNKP detection. Furthermore, the T4 PNKP in cancer cells has been evaluated as a powerful tool for biomedical research and clinical diagnosis, proving a good practical application capacity.

A new fluorescence labeling method for molecular analysis of double-stranded DNA

In this study, a double-stranded DNA (dsDNA) fluorescent labeling method was developed using the fusion proteins of fluorescent protein (FP), and 7 kDa DNA-binding family members including Sso7d from Sulfolobus solfataricus, Aho7c from Acidianus hospitalis, ATSV7 from Acidianus tailed spindle virus and Sto7 from Sulfolobus tokodaii. Using this fluorescent DNA labeling method, we succeeded in single-molecule imaging of bacteriophage λDNA molecules stretched on glass surfaces. The fluorescence of the λDNA with FP fusion proteins decayed 2.4- to 6.4-fold slower than that of the typical intercalating method with SYTOX Green (SxG). In addition, the dynamic behaviors of FP-fused Aho7c-λDNA were relaxed and stretched with and without buffer flow, respectively, in microflow channels and were similar to that with typical intercalating dye, such as YOYO-1 and SxG. this fluorescent DNA labeling method. This fluorescent DNA labeling method can solve the problem of rapid fluorescence decay due to the intercalating dyes and therefore can be expected as an alternative to compound-based fluorescent dye. Thus, this study establishes FP fusion proteins as useful fluorescent DNA probes at the single-molecule level.

Lipoplex-Functionalized Thin-Film Surface Coating Based on Extracellular Matrix Components as Local Gene Delivery System to Control Osteogenic Stem Cell Differentiation.

A gene-activated surface coating is presented as a strategy to design smart biomaterials for bone tissue engineering. The thin-film coating is based on polyelectrolyte multilayerscomposed of collagen I and chondroitin sulfate, two main biopolymers of the bone extracellular matrix, which are fabricated by layer-by-layer assembly. For further functionalization, DNA/lipid-nanoparticles (lipoplexes) are incorporated into the multilayers. The polyelectrolyte multilayer fabrication and lipoplex deposition are analyzed by surface sensitive analytical methods that demonstrate successful thin-film formation, fibrillar structuring of collagen, and homogenous embedding of lipoplexes. Culture of mesenchymal stem cells on the lipoplex functionalized multilayer results in excellent attachment and growth of them, and also, their ability to take up cargo like fluorescence-labelled DNA from lipoplexes. The functionalization of the multilayer with lipoplexes encapsulating DNA encoding for transient expression of bone morphogenetic protein 2 induces osteogenic differentiation of mesenchymal stem cells, which is shown by mRNA quantification for osteogenic genes and histochemical staining. In summary, the novel gene-functionalized and extracellular matrix mimicking multilayer composed of collagen I, chondroitin sulfate, and lipoplexes, represents a smart surface functionalization that holds great promise for tissue engineering constructs and implant coatings to promote regeneration of bone and other tissues.

Chemical Tools for the Study of DNA Repair.

ConspectusDNA repair enzymes continuously provide surveillance throughout our cells, protecting the enclosed DNA from the damage that is constantly arising from oxidation, alkylating species, and radiation. Members of this enzyme class are intimately linked to pathways controlling cancer and inflammation and are promising targets for diagnostics and future therapies. Their study is benefiting widely from the development of new tools and methods aimed at measuring their activities. Here, we provide an Account of our laboratory's work on developing chemical tools to study DNA repair processes in vitro, as well as in cells and tissues, and what we have learned by applying them.We first outline early work probing how DNA repair enzymes recognize specific forms of damage by use of chemical analogs of the damage with altered shapes and H-bonding abilities. One outcome of this was the development of an unnatural DNA base that is incorporated selectively by polymerase enzymes opposite sites of missing bases (abasic sites) in DNA, a very common form of damage.We then describe strategies for design of fluorescent probes targeted to base excision repair (BER) enzymes; these were built from small synthetic DNAs incorporating fluorescent moieties to engender light-up signals as the enzymatic reaction proceeds. Examples of targets for these DNA probes include UDG, SMUG1, Fpg, OGG1, MutYH, ALKBH2, ALKBH3, MTH1, and NTH1. Several such strategies were successful and were applied both in vitro and in cellular settings; moreover, some were used to discover small-molecule modulators of specific repair enzymes. One of these is the compound SU0268, a potent OGG1 inhibitor that is under investigation in animal models for inhibiting hyperinflammatory responses.To investigate cellular nucleotide sanitation pathways, we designed a series of "two-headed" nucleotides containing a damaged DNA nucleotide at one end and ATP at the other; these were applied to studying the three human sanitation enzymes MTH1, dUTPase, and dITPase, some of which are therapeutic targets. The MTH1 probe (ARGO) was used in collaboration with oncologists to measure the enzyme in tumors as a disease marker and also to develop the first small-molecule activators of the enzyme.We proceed to discuss the development of a "universal" probe of base excision repair processes (UBER), which reacts covalently with abasic site intermediates of base excision repair. UBER probes light up in real time as the reaction occurs, enabling the observation of base excision repair as it occurs in live cells and tissues. UBER probes can also be used in efficient and simple methods for fluorescent labeling of DNA. Finally, we suggest interesting directions for the future of this field in biomedicine and human health.