Synthesis and photophysical properties of 7-deaza-2'-deoxyadenosines bearing bipyridine ligands and their Ru(II)-complexes in position 7

Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts

Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

Extended fluorescent uridine analogues: synthesis, photophysical properties and selective interaction with BSA protein

The improvement in fluorescence properties of 2′-deoxyuridine was made possible by the introduction of (hetero)aromatic moieties at the C–5 position of uridine with alkenyl/phenyl/styryl linkers to create a library of useful fluorescent nucleosides.

Synthesis and photophysical evaluation of new fluorescent 7-arylethynyl-7-deazaadenosine analogs

Three new fluorescent 7-deaza-2′-deoxyadenosine analogs were synthesized via the Sonogashira cross-coupling reaction of 7-iodo-7-deaza-2′-deoxyadenosine with 1-ethynylpyrene, 2-ethynyl-6-methoxynaphthalene, and 9-ethynylphenanthrene. The spectral properties of these analogs were evaluated in dioxane, EtOH, and H2O to determine their potential for use as environmentally sensitive fluorescent probes. All three analogs displayed large solvatofluorochromicity in H2O, relative to their emission wavelengths in dioxane or EtOH. Moreover, all three analogs exhibited microenvironmental sensitivity of their fluorescence emission intensity, being moderate to high quantum yields in dioxane and EtOH and significantly lower in H2O. Various attempts to perform domino cross-coupling and annuation reactions on 7-deaza-7-alkynyladenine derivatives to form a new fused tricyclic adenine analog were unsuccessful.

"Chemistry-on-the-complex": functional RuII polypyridyl-type sensitizers as divergent building blocks

Ruthenium polypyridyl type complexes are potent photoactive compounds, and have found - among others - a broad range of important applications in the fields of biomedical diagnosis and phototherapy, energy conversion schemes such as dye-sensitized solar cells (DSSCs) and molecular assemblies for tailored photo-initiated processes. In this regard, the linkage of RuII polypyridyl-type complexes with specific functional moieties is highly desirable to enhance their inherent photophysical properties, e.g., with a targeting function to achieve cell selectivity, or with a dye or redox-active subunits for energy- and electron-transfer. However, the classical approach of performing ligand syntheses first and the formation of Ru complexes in the last steps imposes synthetic limitations with regard to tolerating functional groups or moieties as well as requiring lengthy convergent routes. Alternatively, the diversification of Ru complexes after coordination (termed "chemistry-on-the-complex") provides an elegant complementary approach. In addition to the Click chemistry concept, the rapidly developing synthesis and purification methodologies permit the preparation of Ru conjugates via amidation, alkylation and cross-coupling reactions. In this regard, recent developments in chromatography shifted the limits of purification, e.g., by using new commercialized surface-modified silica gels and automated instrumentation. This review provides detailed insights into applying the "chemistry-on-the-complex" concept, which is believed to stimulate the modular preparation of unpreceded molecular assemblies as well as functional materials based on Ru-based building blocks, including combinatorial approaches.

Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives

Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as electron transfer or the construction of nanomaterials. Among the different metal complexes coupled to oligonucleotides, ruthenium complexes, have been extensively studied due to their remarkable properties. The resulting DNA-ruthenium bioconjugates have already demonstrated their potency in numerous applications. Consequently, this review focuses on the recent synthetic methods developed for the preparation of ruthenium complexes covalently linked to oligonucleotides. In addition, the usefulness of such conjugates will be highlighted and their applications from nanotechnologies to therapeutic purposes will be discussed.

Fluorescent nucleobases as tools for studying DNA and RNA

Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.

Novel water-soluble phosphatriazenes: versatile ligands for Suzuki–Miyaura, Sonogashira and Heck reactions of nucleosides

Two new water-soluble phosphatriazene as versatile ligands for catalyzing Suzuki–Miyaura reactions of purines and pyrimidines in neat water with the possibility of recycling. Copper-free Sonogashira and Heck reaction were also made possible.

Development of ruthenium-based complexes as anticancer agents: toward a rational design of alternative receptor targets

In the search for novel anticancer agents, the development of metal-based complexes that could serve as alternatives to cisplatin and its derivatives has received considerable attention in recent years. This becomes necessary because, at present, cisplatin and its derivatives are the only coordination complexes being used as anticancer agents in spite of inherent serious side effects and their limitation against metastasized platinum-resistant cancer cells. Although many metal ions have been considered as possible alternatives to cisplatin, the most promising are ruthenium (Ru) complexes and two Ru compounds, KP1019 and NAMI-A, which are currently in phase II clinical trials. The major obstacle against the rational design of these compounds is the fact that their mode of action in relation to their therapeutic activities and selectivity is not fully understood. There is an urgent need to develop novel metal-based anticancer agents, especially Ru-based compounds, with known mechanism of actions, probable targets, and pharmacodynamic activity. In this paper, we review the current efforts in developing metal-based anticancer agents based on promising Ru complexes and the development of compounds targeting receptors and then examine the future prospects.

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.

New developments in direct functionalization of C–H and N–H bonds of purine bases via metal catalyzed cross-coupling reactions

This review provides a concise overview on the cross-coupling reactions in direct functionalization of purine bases in recent years.

Design and synthesis of fluorescent 7-deazaadenosine nucleosides containing π-extended diarylacetylene motifs

A novel series of C-modified π-extended 7-deazaadenosines exhibit promising fluorescence properties.

Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review

Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.

Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides

Nucleoside analogues have attracted much attention due to their potential biological activities.

Syntheses and photophysical properties of 5'-6-locked fluorescent nucleosides

Nine fluorescent 5'-6-locked nucleosides were synthesized by condensation of various 1,2-diketones with 5-amino-2'-deoxycytidine. The nucleosides have different substituents on the pyrazine core structure, ranging from two methyl groups to polyaromatic rings. The photophysical properties of each nucleoside were determined, with the nucleosides displaying diverse absorption and emission maxima, extinction coefficients and quantum yields. The nucleoside with the highest fluorescence brightness was phosphitylated and incorporated into an oligonucleotide by means of automated oligonucleotide synthesis. The labelled oligonucleotide in aqueous buffer exhibited a substantially lowered extinction coefficient and quantum yield compared to the nucleoside in THF. The photophysical properties of the nucleoside were also compared in different DNA structural contexts, a single strand, a 14-mer duplex, a 14-mer duplex with an 11-mer overhang, and a 25-mer nicked duplex labelled at the nick site. Circular dichroism and melting temperature studies verified that the nucleoside did not perturb or destabilize the DNA helixes. In fact, when incorporated at the nick site, the nucleoside was found to stabilize the nicked duplex notably compared to its unmodified counterpart. The brightness of the fluorescent nucleoside in DNA increased as the polarity of its surroundings decreased, being highest in the 25-mer nicked duplex where exposure to the polar solvent is minimized by stacking to the adjacent bases on both the 3'- and 5'-side. The nucleosides brightness in the nicked duplex was also found to increase with lowered temperature, in accordance with expected temperature-dependent changes in the stacked-unstacked equilibrium at the nick site.

Synthesis of nucleosides and dNTPs bearing oligopyridine ligands linked through an octadiyne tether, their incorporation into DNA and complexation with transition metal cations

Modified nucleosides (dA(R)s and dC(R)s) bearing bipyridine or terpyridine ligands attached through an octadiyne linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-2'-deoxyadenosine and 5-iodo-2'-deoxycytidine with the corresponding bipyridine- or terpyridine-octadiynes and were triphosphorylated to the corresponding nucleoside triphosphates (dA(R)TPs and dC(R)TPs). The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with divalent metal cations. The complexation of these DNAs containing flexibly-tethered ligands was compared with the previously reported ones bearing rigid acetylene-linked ligands suggesting the possible formation of both inter- and intra-strand complexes with Ni(2+) or Fe(2+).

Rigid 5'-6-locked phenanthroline-derived nucleosides chelated to ruthenium and europium ions

We describe complexes of ruthenium and europium with rigid, 5'-6-locked 1,10-phenanthroline-containing nucleosides. Both nucleosides were synthesized from condensation of 5-amino-2'-deoxycytidine with the corresponding diketone. The ruthenium nucleoside displayed fluorescence characteristic of polypyridine ruthenium complexes with a maximum at 616 nm and a quantum yield of 0.011. Binding of europium to the 1,10-phenanthroline-2,9-diacid moiety of the lanthanide binding nucleoside showed formation of a 1:1 complex with emission at 570-630 nm, whose emission was enhanced by addition of two phenanthroline ligands. The lanthanide-binding nucleoside was incorporated into DNA oligonucleotides and shown to selectively bind one equivalent of europium ions.

Major groove substituents and polymerase recognition of a class of predominantly hydrophobic unnatural base pairs

Expansion of the genetic alphabet with an unnatural base pair is a long-standing goal of synthetic biology. We have developed a class of unnatural base pairs, formed between d5SICS and analogues of dMMO2 that are efficiently and selectively replicated by the Klenow fragment (Kf) DNA polymerase. In an effort to further characterize and optimize replication, we report the synthesis of five new dMMO2 analogues bearing different substituents designed to be oriented into the developing major groove and an analysis of their insertion opposite d5SICS by Kf and Thermus aquaticus DNA polymerase I (Taq). We also expand the analysis of the previously optimized pair, dNaM-d5SICS, to include replication by Taq. Finally, the efficiency and fidelity of PCR amplification of the base pairs by Taq or Deep Vent polymerases was examined. The resulting structure-activity relationship data suggest that the major determinants of efficient replication are the minimization of desolvation effects and the introduction of favorable hydrophobic packing, and that Taq is more sensitive than Kf to structural changes. In addition, we identify an analogue (dNMO1) that is a better partner for d5SICS than any of the previously identified dMMO2 analogues with the exception of dNaM. We also found that dNaM-d5SICS is replicated by both Kf and Taq with rates approaching those of a natural base pair.

Synthesis of nucleoside mono- and triphosphates bearing oligopyridine ligands, their incorporation into DNA and complexation with transition metals

Modified nucleoside mono- (dA(R)MPs and dC(R)MPs) and triphosphates (dA(R)TPs and dC(R)TPs) bearing bipyridine or terpyridine ligands attached via acetylene linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-dAMP or -dATP, and 5-iodo-dCMP or -dCTP with the corresponding bipyridine- or terpyridine-linked acetylenes. The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with Fe(2+).

Pyrrolyl-, 2-(2-thienyl)pyrrolyl- and 2,5-bis(2-thienyl)pyrrolyl-nucleosides: synthesis, molecular and electronic structure, and redox behaviour of C5-thymidine derivatives

A series of modified nucleosides based on thymidine have been prepared by Pd-catalysed cross-coupling between N-alkyl-alkynyl functionalised pyrrolyl- (py), 2-(2-thienyl)pyrrolyl- (tp) or 2,5-bis(2-thienyl)pyrrolyl (tpt) groups with 5-iodo-2'-deoxyuridine. The length of the alkyl chain linking the nucleoside and pyrrolyl-containing unit, N(CH(2))(n)C[triple bond, length as m-dash]C-nucleoside (where n = 1-3) was also varied. The compounds have been characterised by (1)H NMR, ES-MS, UV-vis, cyclic voltammetry (CV) and, in some cases, single-crystal X-ray diffraction. Cyclic voltammetry studies demonstrated that all the py-, tp- and tpt-alkynyl derivatives 1-7 can be electrochemically polymerised to form conductive materials. It was found that increasing the N-alkyl chain length in these cases resulted in only minor changes in the oxidation potential. The same behaviour was observed for the tp- and tpt-modified nucleosides 9-12; however, the py-derivative, 8, produced a poorly conducting material. DFT calculations on the one-electron oxidised cation of the modified nucleosides bearing tp or tpt showed that spin density is located on the pyrrolyl and thienyl units in all cases and that the coplanarity of adjacent rings increases upon oxidation. In contrast, in the corresponding pyrrolyl cases the spin density is distributed over the whole molecule, suggesting that polymerisation does not occur solely at the pyrrolyl-Cα position and the conjugation is interrupted.

Synthesis of nucleoside and nucleotide conjugates of bile acids, and polymerase construction of bile acid-functionalized DNA

Aqueous Sonogashira cross-coupling reactions of 5-iodopyrimidine or 7-iodo-7-deazaadenine nucleosides with bile acid-derived terminal acetylenes linked via an ester or amide tether gave the corresponding bile acid-nucleoside conjugates. Analogous reactions of halogenated nucleoside triphosphates gave directly bile acid-modified dNTPs. Enzymatic incorporation of these modified nucleotides to DNA was successfully performed using Phusion polymerase for primer extension. One of the dNTPs (dCTP bearing cholic acid) was also efficient for PCR amplification.

Base-modified DNA labeled by [Ru(bpy)(3)](2+) and [Os(bpy)(3)](2+) complexes: construction by polymerase incorporation of modified nucleoside triphosphates, electrochemical and luminescent properties, and applications

Modified 2'-deoxynucleoside triphosphates (dNTPs) bearing [Ru(bpy)(3)](2+) and [Os(bpy)(3)](2+) complexes attached via an acetylene linker to the 5-position of pyrimidines (C and U) or to the 7-position of 7-deazapurines (7-deaza-A and 7-deaza-G) have been prepared in one step by aqueous cross-couplings of halogenated dNTPs with the corresponding terminal acetylenes. Polymerase incorporation by primer extension using Vent (exo-) or Pwo polymerases gave DNA labeled in specific positions with Ru(2+) or Os(2+) complexes. Square-wave voltammetry could be efficiently used to detect these labeled nucleic acids by reversible oxidations of Ru(2+/3+) or Os(2+/3+). The redox potentials of the Ru(2+) complexes (1.1-1.25 V) are very close to that of G oxidation (1.1 V), while the potentials of Os(2+) complexes (0.75 V) are sufficiently different to enable their independent detection. On the other hand, Ru(2+)-labeled DNA can be independently analyzed by luminescence. In combination with previously reported dNTPs bearing ferrocene, aminophenyl, and nitrophenyl tags, the Os-labeled dATP has been successfully used for "multicolor" redox labeling of DNA and for DNA minisequencing.