Fluorogenic, Catalytic, Photochemical Reaction for Amplified Detection of Nucleic Acids

Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies

The expanding scope of chemical reactions applied to nucleic acids has diversified the design of nucleic acid-based technologies that are essential to medicinal chemistry and chemical biology. Among chemical reactions, visible light photochemical reaction is considered a promising tool that can be used for the manipulations of nucleic acids owing to its advantages, such as mild reaction conditions and ease of the reaction process. Of late, inspired by the development of visible light-absorbing molecules and photocatalysts, visible light-driven photochemical reactions have been used to conduct various molecular manipulations, such as the cleavage or ligation of nucleic acids and other molecules as well as the synthesis of functional molecules. In this review, we describe the recent developments (from 2010) in visible light photochemical reactions involving nucleic acids and their applications in the design of nucleic acid-based technologies including DNA photocleaving, DNA photoligation, nucleic acid sensors, the release of functional molecules, and DNA-encoded libraries.

Red light-triggered photoreduction on a nucleic acid template

Conjugate Sn(iv)(pyropheophorbide a)dichloride-(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templated photoreduction. It is highly sensitive to single mismatches in the NA-template and can detect down to 5 nM NAs.

Acenes beyond organic electronics: sensing of singlet oxygen and stimuli-responsive materials

Although they are often detrimental in organic electronics, the cycloaddition reactions of acenes, especially with singlet oxygen, are useful in a range of responsive materials.

Red light-triggered nucleic acid-templated reaction based on cyclic oligonucleotide substrates

A red light-triggered reaction based on cyclic oligonucleotide substrates that is accelerated over 30-fold by specific nucleic acid templates and generates a bright fluorescent probe was developed. We confirmed that this reaction is compatible with fluorescence correlation spectroscopy (FCS) thereby allowing detection of nucleic acids down to 1 nM.

Red Light Triggered Fluorogenic Reaction with Picomolar Sensitivity Toward Nucleic Acids

We have previously reported on a red light triggered, singlet oxygen-mediated fluorogenic reaction that is templated in a highly sequence specific fashion by nucleic acids (S. Dutta, A. Fulop, A. Mokhir, Bioconjgate Chem. 2013, 24 (9), 1533-1542). Up to the present date, it has remained a single templated reaction responsive to nontoxic >650 nm light. However, it is operative only in the presence of relatively high (>2 nM) concentrations of templates that dramatically limit its applicability in nucleic acid detection. In the current work, we established that an inefficient intermolecular electron transfer involved in reduction of the 1,4-endoperoxide intermediate, formed in the rate-limiting reaction step, is responsible for inhibition of the reaction at low reagent concentrations. We suggested the solution of the problem which includes a combination of a cleavable (9-alkoxyanthracene) moiety with a two-electron donating fragment in one molecule. This approach enables the efficient intramolecular electron transfer to the endoperoxide intermediate in the critical reaction step. Due to the intramolecular character of the latter process, it is practically independent of concentration of the reagents. The reaction based on the improved cleavable moiety was found to be >200-fold more sensitive than the previously reported one. It is fast, sequence specific, and compatible with live cells. Accounting for short reactions times (<30 min), nontoxic trigger (red light), excellent sensitivity, and sequence specificity, this is presently the best reported photochemical templated reaction compatible with live cells.

Oxo-Functionalized Graphene as a Cell Membrane Carrier of Nucleic Acid Probes Controlled by Aging

We applied a fluorescein-containing oligonucleotide (ON) to probe surface properties of oxidized graphene (oxo-G) and observed that graphene-like patches are formed upon aging of oxo-G, indicated by enhanced probe binding and by FTIR spectroscopic analysis. By using a recently developed fluorogenic endoperoxide (EP) probe, we confirmed that during the aging process the amount of EPs on the oxo-G surface is reduced. Furthermore, aging was found to strongly affect cell membrane carrier properties of this material. In particular, freshly prepared oxo-G does not act as a carrier, whereas oxo-G aged for 28 days at 4 °C is an excellent carrier. Based on these data we prepared an optimized oxo-G, which has a low-defect density, binds ONs, is not toxic, and acts as cell membrane carrier. We successfully applied this material to design fluorogenic probes of representative intracellular nucleic acids 28S rRNA and β-actin-mRNA. The results will help to standardize oxidized graphene derivatives for biomedical and bioanalytical applications.

DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes

Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.

Red light-controlled polymerase chain reaction

A 23-mer DNA “caged” at its 3′-terminus with a 9-anthracenyl moiety was prepared.

Singlet oxygen in DNA nanotechnology

CONSPECTUS: Singlet oxygen ((1)O2), the first excited electronic state of molecular oxygen, is a significant molecule, despite its minute size. For more than half a century, the molecule has been widely used and studied in organic synthesis, due to its characteristic oxygenation reactions. Furthermore, (1)O2 plays a key role in mechanisms of cell death, which has led to its use in therapies for several types of cancer and other diseases. The high abundance of oxygen in air provides a wonderful source of molecules that can be excited to the reactive singlet state, for example, by UV/vis irradiation of a photosensitizer molecule. Although convenient, this oxygen abundance also presents some challenges for purposes that require (1)O2 to be generated in a controlled manner. In the past decade, we and others have employed DNA nanostructures to selectively control and investigate the generation, lifetime, and reactions of (1)O2. DNA-based structures are one of the most powerful tools for controlling distances between molecules on the nanometer length scale, in particular for systems that closely resemble biological settings, due to their inherent ability to specifically form duplex structures with well-defined and predictable geometries. Here, we present some examples of how simple DNA structures can be employed to regulate (1)O2 production by controlling the behavior of (1)O2-producing photosensitizers through their interactions with independent quencher molecules. We have developed different DNA-based systems in which (1)O2 production can be switched ON or OFF in the presence of specific DNA sequences or by changing the pH of the solution. To further illustrate the interplay between DNA structures and (1)O2, we present three pieces of research, in which (1)O2 is used to activate or deactivate DNA-based systems based on the reaction between (1)O2 and cleavable linkers. In one example, it is demonstrated how a blocked oligonucleotide can be released upon irradiation with light of a specific wavelength. In more complex systems, DNA origami structures composed of more than 200 individual oligonucleotides were employed to study (1)O2 reactions in spatially resolved experiments on the nanoscale.

Nucleic acid-specific photoactivation of oligodeoxyribonucleotides labeled with deuterated dihydro-N,N,N',N'-tetramethylrhodamine using green light

We developed a simple protocol for high-yielding synthesis of conjugates of a deuterated dihydro-N,N,N',N'-tetramethylrhodamine (F*) with oligodeoxyribonucleotides and a 2'-OMe RNA (a representative nuclease-resistant, chemically modified oligonucleotide) using easily accessible starting materials including NaBD4 and conjugates of oligonucleotides with N,N,N',N'-tetramethylrhodamine (F). These compounds were found to be stable in air and insensitive to light at 525, 635 and 650 nm, whereas slow activation occurs upon their exposure to 470 nm light. However, at the conditions of the templated reaction, in the presence of a target nucleic acid and a photocatalyst based on the eosin structure, the F* is oxidized forming fluorescent F. This reaction is >30-fold faster than the background reaction in the absence of the template. Moreover, the presence of a single mismatch in the target nucleic acid slows down the templated reaction by eightfold. These activatable dyes can potentially find applications as nucleic acid-specific probes for super-resolution imaging in live cells.

Amplification by nucleic acid-templated reactions

Nucleic acid-templated reactions that proceed with turnover provide a means for signal amplification, which facilitates the use and detection of biologically occurring DNA/RNA molecules.