"Double click" reaction on 7-deazaguanine DNA: synthesis and excimer fluorescence of nucleosides and oligonucleotides with branched side chains decorated with proximal pyrenes

5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts

The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.

A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids

Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.

Alkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†

The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by Sonogashira cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition. The copper(I)-catalyzed click reaction on the tripropargylamino nucleoside was significantly faster and higher yielding than that for nucleosides carrying linear alkynyl chains. Also, this reaction could be performed with copper(II) as the catalyst. An autocatalyzed cycle was suggested in which the click product acts as a catalyst. Pyrene click adducts of linear alkynylated nucleosides showed pyrene monomer emission, while tripropargylamino adducts showed monomer and excimer fluorescence. The fluorescence intensities of the 5-aza-7-deazaguanine nucleosides were higher than those of their 7-deazaguanine counterparts. The reported clickable nucleosides can be utilized to functionalize or to cross-link monomeric nucleosides or DNA for diagnostic or imaging purposes and other applications in nucleic acid chemistry and biotechnology.

Microfluidic Preconcentration Chip with Self-Assembled Chemical Modified Surface for Trace Carbonyl Compounds Detection

Carbonyl compounds in water sources are typical characteristic pollutants, which are important indicators in the health risk assessment of water quality. Commonly used analytical chemistry methods face issues such as complex operations, low sensitivity, and long analysis times. Here, we report a silicon microfluidic device based on click chemical surface modification that was engineered to achieve rapid, convenient and efficient capture of trace level carbonyl compounds in liquid solvent. The micro pillar arrays of the chip and microfluidic channels were designed under the basis of finite element (FEM) analysis and fabricated by the microelectromechanical systems (MEMS) technique. The surface of the micropillars was sputtered with precious metal silver and functionalized with the organic substance amino-oxy dodecane thiol (ADT) by self-assembly for capturing trace carbonyl compounds. The detection of ppb level fluorescent carbonyl compounds demonstrates that the strategy proposed in this work shows great potential for rapid water quality testing and for other samples with trace carbonyl compounds.

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells

Despite the broad applicability of the Huisgen cycloaddition reaction, the click functionalization of RNAs with peptides still remains a challenge. Here we describe a straightforward method for the click functionalization of siRNAs with peptides of different sizes and complexities. Among them, a promising peptide carrier for the selective siRNA delivery into HER2+ breast cancer cell lines has been reported.

Fluorogenic “photoclick” labelling of DNA using a Cy3 dye

Two 2′-deoxyuridines as new building blocks for automated DNA synthesis carry a small aryltetrazole as a “photoclickable” group at their 5-positions.

MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents

DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–Hg^II–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.

Minor Groove 3-Deaza-Adenosine Analogues: Synthesis and Bypass in Translesion DNA Synthesis

Anticancer drugs that alkylate DNA in the minor groove may give rise to 3-alkyl-adenosine adducts that interfere with replication, inducing apoptosis in rapidly dividing cancer cells. However, translesion DNA synthesis (TLS) by polymerase enzymes (Pols) with the capacity to bypass DNA adducts may contribute to damage tolerance and drug resistance. 3-Alkyl-adenosine adducts are unstable and depurinate, which is a barrier to addressing chemical and enzymatic aspects of how they impact the progress of DNA Pols. To characterize structure-based relationships of 3-adenine alkylation relevant to cancer drugs on duplex stability and DNA Pol-catalyzed DNA synthesis, we synthesized stable 3-deaza-3-alkyl-adenosine analogues, including 3-deaza-3-phenethyl-adenosine and 3-deaza-3-methoxynaphthylethyl-adenosine, and incorporated them into oligonucleotides. A moderate reduction of duplex stability was observed on the basis of thermal denaturation data. Replication studies using purified Y-family human DNA Pols hPol η, κ, and ι indicated that these enzymes can perform TLS over the modified bases. hPol η had higher misincorporation rates when synthesizing opposite the modified bases compared with adenine, whereas hPol κ and ι maintained high fidelity. These results provide insight into how alterations in chemical structure reduce bypass of minor-groove adducts, and provide novel chemical probes for evaluating minor-groove DNA alkylation.

Synthesis of 8-(1,2,3-triazol-1-yl)-7-deazapurine nucleosides by azide-alkyne click reactions and direct C-H bond functionalization

Treatment of toyocamycin or sangivamycin with 1,3-dibromo-5,5-dimethylhydantoin in MeOH (r.t./30 min) gave 8-bromotoyocamycin and 8-bromosangivamycin in good yields. Nucleophilic aromatic substitution of 8-bromotoyocamycin with sodium azide provided novel 8-azidotoyocamycin. Strain promoted click reactions of the latter with cyclooctynes resulted in the formation of the 1,2,3-triazole products. Iodine-mediated direct C8-H bond functionalization of tubercidin with benzotriazoles in the presence of tert-butyl hydroperoxide gave the corresponding 8-benzotriazolyltubercidin derivatives. The 8-(1,2,3-triazol-1-yl)-7-deazapurine derivatives showed moderate quantum yields and a large Stokes shifts of ~ 100 nm.

Sensitive Detection of Single-Nucleotide Mutation in the BRAF Mutation Site (V600E) of Human Melanoma Using Phosphate-Pyrene-Labeled DNA Probes

A series of novel nucleotide phosphoramidites were rationally designed and synthesized and were then site-specifically incorporated in DNA oligonucleotide probes with pyrene-modified phosphate. These oligodeoxynucleotide (ODN) probes almost have no inherent fluorescence emission with pyrene modification at 3' phosphate of corresponding nucleotides as a result of the photoinduced electron-transfer quenching effect of nucleobases (thymidine ∼ cytidine > guanosine ≫ adenosine). However, strong fluorescence emission was observed only with the perfectly matched duplex for the probes with pyrene modified at 3' phosphate of thymidine and cytidine. These rationally designed ODN probes successfully worked as "turn on" fluorescence oligonucleotide sensors for single-nucleotide polymorphism (SNP) and were used for detecting a single BRAF mutation site (V600E) of human melanoma.

Synthesis and photophysical properties of pyrene-labeled 3-deaza-2'-deoxyadenosines comprising a non-π-conjugated linker: fluorescence quenching-based oligodeoxynucleotide probes for thymine identification

Pyrene-labeled 3-deaza-2'-deoxyadenosine comprising a non-π-conjugated linker (py3z)A (1) was synthesized and its photophysical properties were investigated. Oligodeoxynucleotide (ODN) probes containing (py3z)A (1) exhibited remarkable fluorescence quenching only when the opposite base of the complementary strand was the perfectly matched thymine. Such fluorescence quenching-based ODN probes exhibited excellent on-off switching properties, making them useful tools for single nucleotide polymorphism (SNP) genotyping and for the identification of target genes and structural studies of nucleic acids.

5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts

Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides

Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

"Photoclick" postsynthetic modification of DNA

A new DNA building block bearing a push-pull-substituted diaryltetrazole linked to the 5-position of 2'-deoxyuridine through an aminopropynyl group was synthesized. The accordingly modified oligonucleotide allows postsynthetic labeling with a maleimide-modified sulfo-Cy3 dye, N-methylmaleimide, and methylmethacrylate as dipolarophiles by irradiation at 365 nm (LED). The determined rate constant of (23±7) M(-1)  s(-1) is remarkably high with respect to other copper-free bioorthogonal reactions and comparable with the copper-catalyzed cycloaddition between azides and acetylenes.

Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers

Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.

2'-Bispyrene-modified 2'-O-methyl RNA probes as useful tools for the detection of RNA: synthesis, fluorescent properties, and duplex stability

The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs.

C5-alkynyl-functionalized α-L-LNA: synthesis, thermal denaturation experiments and enzymatic stability

Major efforts are currently being devoted to improving the binding affinity, target specificity, and enzymatic stability of oligonucleotides used for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. One of the most popular strategies toward this end has been to introduce additional modifications to the sugar ring of affinity-inducing conformationally restricted nucleotide building blocks such as locked nucleic acid (LNA). In the preceding article in this issue, we introduced a different strategy toward this end, i.e., C5-functionalization of LNA uridines. In the present article, we extend this strategy to α-L-LNA: i.e., one of the most interesting diastereomers of LNA. α-L-LNA uridine monomers that are conjugated to small C5-alkynyl substituents induce significant improvements in target affinity, binding specificity, and enzymatic stability relative to conventional α-L-LNA. The results from the back-to-back articles therefore suggest that C5-functionalization of pyrimidines is a general and synthetically straightforward approach to modulate biophysical properties of oligonucleotides modified with LNA or other conformationally restricted monomers.

Efficient synthesis of pyrene-1-carbothioamides and carboxamides. Tunable solid-state fluorescence of pyrene-1-carboxamides

This paper discloses efficient synthesis of pyrene-1-carbothioamides and carboxamides via Friedel–Crafts reaction of pyrene with isocyanates followed by oxidative desulfuration. The amides display solid-state fluorescence with quantum yields up to 62%, originating from monomers, aggregates or excimers.

Recognition of mixed-sequence DNA duplexes: design guidelines for invaders based on 2'-O-(pyren-1-yl)methyl-RNA monomers

The development of agents that recognize mixed-sequence double-stranded DNA (dsDNA) is desirable because of their potential as tools for detection, regulation, and modification of genes. Despite progress with triplex-forming oligonucleotides, peptide nucleic acids, polyamides, and other approaches, recognition of mixed-sequence dsDNA targets remains challenging. Our laboratory studies Invaders as an alternative approach toward this end. These double-stranded oligonucleotide probes are activated for recognition of mixed-sequence dsDNA through modification with +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl-RNA monomers and have recently been shown to recognize linear dsDNA, DNA hairpins, and chromosomal DNA. In the present work, we systematically studied the influence that the nucleobase moieties of the 2'-O-(pyren-1-yl)methyl-RNA monomers have on the recognition efficiency of Invader duplexes. Results from thermal denaturation, binding energy, and recognition experiments using Invader duplexes with different +1 interstrand zippers of the four canonical 2'-O-(pyren-1-yl)methyl-RNA A/C/G/U monomers show that incorporation of these motifs is a general strategy for activation of probes for recognition of dsDNA. Probe duplexes with interstrand zippers comprising C and/or U monomers result in the most efficient recognition of dsDNA. The insight gained from this study will drive the design of efficient Invaders for applications in molecular biology, nucleic acid diagnostics, and biotechnology.

Ethynyl side chain hydration during synthesis and workup of "clickable" oligonucleotides: bypassing acetyl group formation by triisopropylsilyl protection

Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases.

Dual isotope labeling: conjugation of 32P-oligonucleotides with 18F-aryltrifluoroborate via copper(I) catalyzed cycloaddition

A one-pot-two-step labeling of an oligonucleotide with an (18)F-ArBF3(-)(aryltrifluoroborate) radioprosthetic is reported herein. In order to characterize labeling in terms of radiochemistry, phosphorus-32 was also introduced to the 5'-terminus of the oligonucleotide via enzymatic phosphorylation. A pendant azide group was subsequently conjugated to the 5'-phosphate of the oligonucleotide. Copper(I) catalyzed [2+3] cycloaddition was undertaken to conjugate an alkyne-bearing(18)F-ArBF3(-) to the oligonucleotide. Following polyacrylamide gel electrophoresis, this doubly-labeled bioconjugate exhibited decay properties of both the phosphorus-32 and fluorine-18, that were confirmed by autoradiography at selected lengths of time, which in turn provided concrete evidence of successful conjugation. These results are corroborated by HPLC analysis of the labeled material. Taken together this work demonstrates viable use of (18)F-ArBF3(-) prosthetics for labeling oligonucleotides for use in PET imaging.

Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA

The development of synthetic agents that recognize double-stranded DNA (dsDNA) is a long-standing goal that is inspired by the promise for tools that detect, regulate, and modify genes. Progress has been made with triplex-forming oligonucleotides, peptide nucleic acids, and polyamides, but substantial efforts are currently devoted to the development of alternative strategies that overcome the limitations observed with the classic approaches. In 2005, we introduced Invader locked nucleic acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through modification with "+1 interstrand zippers" of 2'-N-(pyren-1-yl)methyl-2'-amino-α-l-LNA monomers. Despite promising preliminary results, progress has been slow because of the synthetic complexity of the building blocks. Here we describe a study that led to the identification of two simpler classes of Invader monomers. We compare the thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2'-amino-α-l-LNA, 2'-N-methyl-2'-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling, and NMR spectroscopy are used to elucidate the structural factors that govern probe activation. We demonstrate that probes with +1 zippers of 2'-O-(pyren-1-yl)methyl-RNA or 2'-N-methyl-2'-N-(pyren-1-yl)methyl-2'-amino-DNA monomers recognize DNA hairpins with similar efficiency as original Invader LNAs. Access to synthetically simple monomers will accelerate the use of Invader-mediated dsDNA recognition for applications in molecular biology and nucleic acid diagnostics.

Control of aggregation-induced emission by DNA hybridization

Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.

Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry

There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.

Three pyrene-modified nucleotides: synthesis and effects in secondary nucleic acid structures

Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.

A ratiometric fluorescent on-off Zn2+ chemosensor based on a tripropargylamine pyrene azide click adduct

A new, easy-to-prepare and highly selective pyrene-linked tris-triazole amine fluorescent chemosensor has been designed from tripropargylamine and pyrene azide using Cu(I)-catalyzed click chemistry. The fluorescence on-off sensor 1 is highly selective for Zn(2+) displaying a ratiometric change in emission. The relative intensity ratio of monomer to excimer fluorescence (M(376)/E(465)) of the sensor increases 80-fold upon the addition of 10 equiv of Zn(2+) ions (with a detection limit of 0.2 μM).

Construction and assembly of branched Y-shaped DNA: "click" chemistry performed on dendronized 8-aza-7-deazaguanine oligonucleotides

Branched DNA was synthesized from tripropargylated oligonucleotides by the Huisgen-Meldal-Sharpless cycloaddition using "stepwise and double click" chemistry. Dendronized oligonucleotides decorated with 7-tripropargylamine side chains carrying two terminal triple bonds were further functionalized with bis-azides to give derivatives with two terminal azido groups. Then, the branched side chains with two azido groups or two triple bonds were combined with DNA-fragments providing the corresponding clickable function. Both concepts afforded branched (Y-shaped) three-armed DNA. Annealing of branched DNA with complementary oligonucleotides yielded supramolecular assemblies. The concept of "stepwise and double click" chemistry combined with selective hybridization represents a flexible tool to generate DNA nanostructures useful for various purposes in DNA diagnostics, delivery, and material science applications.

Additional insights into luminescence process of polycyclic aromatic hydrocarbons with carbonyl groups: photophysical properties of secondary N-alkyl and tertiary n,n-dialkyl carboxamides of naphthalene, anthracene, and pyrene

Here we report the substitution effects of N-alkyl and N,N-dialkyl carboxamide groups on the fluorescence properties of polycyclic aromatic hydrocarbon chromophores, so as to control their fluorescence properties. The fluorescence properties of compounds obtained using solvents with different polarities showed very little change, indicating that the modified compounds do not form charge transfer states. TD-DFT calculations and measurements performed at low temperature (78 K) and in viscous solvents revealed that the N-alkyl and N,N-dialkyl carboxamide groups tend to reduce the contributions from intersystem crossing and increase those from internal conversion. Considering that the fluorescence mechanism of low-fluorescence carbonyl compounds such as aldehyde and ketone is dominated by intersystem crossing and that of high-luminescence carbonyl compounds such as carboxylic acid and ester is dominated by a radiative process, it can be said that the photophysical process of N-alkyl and N,N-dialkyl carboxamides is novel. In addition, the calculation results for excited states indicated that such contributions can be controlled by selecting the appropriate polycyclic aromatic hydrocarbon or amide structure, in addition to solvent viscosity and temperature.