Building-Block Approach for the Straightforward Incorporation of a New FRET (Fluorescence-Resonance-Energy Transfer) System into Synthetic DNA

Electronic Relaxation Dynamics in 2-Quinolinones with Extended Conjugation

The 2-quinolinone family of molecules, also known as carbostyrils, have been proposed as light absorbing donor molecules in energy transfer based sensing schemes and as possible photocatalysts. Both of these applications make use of electronic excited states, but the photophysics of 2-quinolinones have not yet been examined closely. This study applies static and dynamic spectroscopy, with supporting density functional theory calculations, to reveal the electronic relaxation dynamics of a family of five 2-quinolinones with extended conjugated rings. These modifications lead to red-shifted absorbance and emission maxima, relative to unmodified 2-quinolinone. Optical excitation of these molecules with near UV light resulted in transitions with strong π → π* and HOMO → LUMO character. Time-correlated single photon counting measurements yielded fluorescence lifetimes ranging from 849.3 (±0.6) ps to 4.586 (±0.002) ns. Transient absorption spectroscopy revealed relaxation dynamics of the S₁ excited state formed by photoexcitation at 350 nm, along with formation of a long-lived signal assigned as excited state absorption by a triplet excited state. Vibrational relaxation in the S₁ state was also characterized in some compounds. Overlapping signals of S₁ decay and triplet growth in the transient absorption data set could not be fully disentangled. These results demonstrate a highly competitive relaxation scheme following multiple simultaneous pathways, a promising situation for establishing chemical control of electronic relaxation in the 2-quinolinone family.

Facile Access to Bromonucleosides Using Sodium Monobromoisocyanurate (SMBI)

Bromonucleosides constitute a significant class of molecules and are well known for their biological activity. 5-Bromouridine, 5-bromo-2'-deoxyuridine, 5-bromouridine-5'-triphosphate, and nucleotides containing 5-bromouridine have been tested and used for numerous biological studies. 8-Bromopurine nucleosides have been used as essential precursors for the synthesis of nucleosides with fluorescent properties. This unit describes protocols for the synthesis of bromonucleosides using sodium monobromoisocyanurate (SMBI) in a straightforward way. Reactions are carried out at room temperature, and aqueous solvent mixtures are used to dissolve the nucleosides. Sodium azide is used as catalyst for the bromination of pyrimidine nucleosides, and no catalyst is necessary for the bromination of purine nucleosides. Unprotected 2'-deoxy pyrimidine and 2'-deoxy purine nucleosides are treated with SMBI to afford C-5 bromo pyrimidine and C-8 bromo purine nucleosides, respectively. This methodology has been found to be efficient for the synthesis of bromonucleosides on gram scale with consistently high yields. © 2017 by John Wiley & Sons, Inc.

C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability

Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.

Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers

LNA and nucleobase-modified DNA monomers are two types of building blocks that are used extensively in oligonucleotide chemistry. However, there are only very few reports in which these two monomer families are used alongside each other. In the present study we set out to characterize the biophysical properties of oligodeoxyribonucleotides in which C5-modified 2'-deoxyuridine or C8-modified 2'-deoxyadenosine monomers are flanked by LNA nucleotides. We hypothesized that the LNA monomers would alter the sugar rings of the modified DNA monomers toward more RNA-like North-type conformations for maximal DNA/RNA affinity and specificity. Indeed, the incorporation of LNA monomers almost invariably results in increased target affinity and specificity relative to the corresponding LNA-free ONs, but the magnitude of the stabilization varies greatly. Introduction of LNA nucleotides as direct neighbors into C5-pyrene-functionalized pyrimidine DNA monomers yields oligonucleotide probes with more desirable photophysical properties as compared to the corresponding LNA-free probes, including more intense fluorescence emission upon target binding and improved discrimination of single nucleotide polymorphisms (SNPs). These hybrid oligonucleotides are therefore promising probes for diagnostic applications.

Metal-free ring expansion of indoles with nitroalkenes: a simple, modular approach to 3-substituted 2-quinolones

3-Substituted 2-quinolones are obtained via a novel metal-free transannulation reaction of 2-nitroolefins with 2-substituted indoles in polyphosphoric acid.

Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers

Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.

Metal-free transannulation reaction of indoles with nitrostyrenes: a simple practical synthesis of 3-substituted 2-quinolones

3-Substituted 2-quinolones are obtained via a novel, metal-free transannulation reaction of 2-substituted indoles with 2-nitroalkenes in polyphosphoric acid. The reaction can be used in conjunction with the Fisher indole synthesis offering a practical three-component heteroannulation methodology to produce 2-quinolones from arylhydrazines, 2-nitroalkenes and acetophenone.

An efficient and facile methodology for bromination of pyrimidine and purine nucleosides with sodium monobromoisocyanurate (SMBI)

An efficient and facile strategy has been developed for bromination of nucleosides using sodium monobromoisocyanurate (SMBI). Our methodology demonstrates bromination at the C-5 position of pyrimidine nucleosides and the C-8 position of purine nucleosides. Unprotected and also several protected nucleosides were brominated in moderate to high yields following this procedure.

Bromination at C-5 of Pyrimidine and C-8 of Purine Nucleosides with 1,3-Dibromo-5,5-dimethylhydantoin

Treatment of the protected and unprotected nucleosides with 1,3-dibromo-5,5- dimethylhydantoin in aprotic solvents such as CH(2)Cl(2), CH(3)CN, or DMF effected smooth bromination of uridine and cytidine derivatives at C-5 of pyrimidine rings as well as adenosine and guanosine derivatives at C-8 of purine rings. Addition of Lewis acids such as trimethylsilyl trifluoromethanesulfonate enhanced efficiency of bromination.

Novel three-color FRET tool box for advanced protein and DNA analysis

We report on a new three-color FRET system which we were able to verify in peptides as well as in synthetic DNA. All three chromophores could be introduced by a building block approach avoiding postsynthetic labeling. Additional features are robustness, matching spectroscopic properties, high-energy transfer, and sensitivity. The system was investigated in detail on a set of peptides as well as an array of tailored oligonucleotides. The detailed analysis of the experimental data and comparison with theoretical considerations were in excellent agreement. It is shown that in the case of polypeptides specific interaction with the fluorescence probes has to be considered. In contrast with DNA, the fluorescence probes did not show any indications of such interactions. The novel three-color FRET toolbox revealed the potential for applications studying fundamental processes of three interacting molecules in life science applications.

Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. Altogether 13 different double-stranded 30 base pair DNAs showing small incremental differences in the distances between donor and acceptor were synthesized. Using the fluorescence of the donor as well as of the acceptor, D/A separations were determined and compared to those derived from a well-established model for DNA distance calculations. The model calculations and anisotropy studies revealed that the donor can nearly be seen as a free rotator allowing the application of the established FRET data evaluation.

Multimodal coupling of optical transitions and plasmonic oscillations in rhodamine B modified gold nanoparticles

The optical properties of a photoluminescent dye rhodamine B (RhB) interacting with gold nanoparticles (AuNP) have been investigated using plasmonic absorbance, fluorescence, and resonance elastic light scattering (RELS) spectroscopy. We have found that these interactions result in a multimodal coupling that influence optical transitions in RhB. In absorbance measurements, we have observed for the first time the coupling resulting in strong screening of RhB π-π* transitions, likely caused by a contact adsorption of RhB on a conductive surface of AuNP. The nanoparticles quench also very efficiently the RhB fluorescence. We have determined that the static quenching mechanism with a non-Förster fluorescence resonance energy transfer (FRET) from RhB molecules to AuNP is involved. The Stern-Volmer dependence F(0)/F = f(Q) shows an upward deviation from linearity, attributed to the ultra-high quenching efficiency of AuNP leading to the new extended Stern-Volmer model. A sharp RELS peak of RhB alone (λ(max) = 566 nm) has been observed for the first time and attributed to the resonance fluorescence and enhanced scattering. This peak is completely quenched in the presence of AuNP(22nm). Our quantum mechanical calculations confirm that the distance between AuNP surface and conjugated π-electron system in RhB is well within the range of plasmonic fields extending from AuNP. The optical transition coupling to plasmonic oscillations and the efficient energy transfer due to the interactions of fluorescent dyes with nanoparticles are important for biophysical studies of life processes and applications in nanomedicine.

A new assay format for NF-kappaB based on a DNA triple helix and a fluorescence resonance energy transfer

Herein we report a feasibility study for a new concept to detect DNA binding protein NF-kappaB based on a DNA triple helix formation in combination with a fluorescence resonance energy transfer (FRET). The new principle avoids expensive antibodies and radioactivity and might have implications for assays of other DNA binding proteins.

Novel strategies for the site-specific covalent labelling of nucleic acids

To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.