The oxime bond formation as an efficient tool for the conjugation of ruthenium complexes to oligonucleotides and peptides

Fifty Shades of Phenanthroline: Synthesis Strategies to Functionalize 1,10-Phenanthroline in All Positions

1,10-Phenanthroline (phen) is one of the most popular ligands ever used in coordination chemistry due to its strong affinity for a wide range of metals with various oxidation states. Its polyaromatic structure provides robustness and rigidity, leading to intriguing features in numerous fields (luminescent coordination scaffolds, catalysis, supramolecular chemistry, sensors, theranostics, etc.). Importantly, phen offers eight distinct positions for functional groups to be attached, showcasing remarkable versatility for such a simple ligand. As a result, phen has become a landmark molecule for coordination chemists, serving as a must-use ligand and a versatile platform for designing polyfunctional arrays. The extensive use of substituted phenanthroline ligands with different metal ions has resulted in a diverse array of complexes tailored for numerous applications. For instance, these complexes have been utilized as sensitizers in dye-sensitized solar cells, as luminescent probes modified with antibodies for biomaterials, and in the creation of elegant supramolecular architectures like rotaxanes and catenanes, exemplified by Sauvage's Nobel Prize-winning work in 2016. In summary, phen has found applications in almost every facet of chemistry. An intriguing aspect of phen is the specific reactivity of each pair of carbon atoms ([2,9], [3,8], [4,7], and [5,6]), enabling the functionalization of each pair with different groups and leading to polyfunctional arrays. Furthermore, it is possible to differentiate each position in these pairs, resulting in non-symmetrical systems with tremendous versatility. In this Review, the authors aim to compile and categorize existing synthetic strategies for the stepwise polyfunctionalization of phen in various positions. This comprehensive toolbox will aid coordination chemists in designing virtually any polyfunctional ligand. The survey will encompass seminal work from the 1950s to the present day. The scope of the Review will be limited to 1,10-phenanthroline, excluding ligands with more intracyclic heteroatoms or fused aromatic cycles. Overall, the primary goal of this Review is to highlight both old and recent synthetic strategies that find applicability in the mentioned applications. By doing so, the authors hope to establish a first reference for phenanthroline synthesis, covering all possible positions on the backbone, and hope to inspire all concerned chemists to devise new strategies that have not yet been explored.

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.

Efficient Buchwald-Hartwig-Migita Cross-Coupling for DNA Thioglycoconjugation

An efficient method for the thioglycoconjugation of iodinated oligonucleotides by Buchwald-Hartwig-Migita cross-coupling under mild conditions is reported. The method enables divergent synthesis of many different functionalized thioglycosylated ODNs in good yields, without affecting the integrity of the other A, C, and G nucleobases.

Palladium-Mediated Labeling of Nucleic Acids

New applications of Pd-catalyzed coupling reactions (Suzuki-Miyaura, Sonogashira, and Stille-Migita coupling) for post-conjugation of nucleic acids have been developed recently. Breakthroughs in this area might now pave the way for the development of sophisticated DNA probes, which might be of great interest in chemical biology, nanotechnology, and bioanalysis, as well as in diagnostic domains.

Selective chemical modification of DNA with alkoxy- and benzyloxyamines

DNA is modified selectively at cytosine with benzyloxyamine and -derivatives carrying handles for click reactions.

Ru-TAP complexes and DNA: from photo-induced electron transfer to gene photo-silencing in living cells

In this review, examples of applications of the photo-induced electron transfer (PET) process between photo-oxidizing Ru-TAP (TAP = 1,4,5,8-tetraazaphenanthrene) complexes and DNA or oligodeoxynucleotides (ODNs) are discussed. Applications using a free Ru-TAP complex (not chemically anchored to an ODN) are first considered. In this case, the PET gives rise to the production of an irreversible adduct of the Ru complex on a guanine (G) base, with formation of a covalent bond. After absorption of a second photon, this adduct can generate a bi-adduct, whereby the same complex binds to a second G moiety. These bi-adduct formations are responsible for photo-cross-linking between two strands of a duplex, each containing a G base, or between two G moieties of a single strand such as a telomeric sequence, as demonstrated by polyacrylamide gel electrophoresis analyses or mass spectrometry. Scanning force microscopy also allows the detection of such photobridgings with plasmid DNA. Other applications, for example with Ru-ODN, i.e. ODN with chemically anchored Ru-TAP complexes, are also discussed. It is shown that such Ru-ODN probes containing a G base in their own sequences are capable of photo-cross-linking selectively with their targeted complementary sequences, and, in the absence of such targets, they self-photo-inhibit. Such processes are applied successfully in gene photo-silencing of human papillomavirus cancer cells.

Ruthenium oligonucleotides, targeting HPV16 E6 oncogene, inhibit the growth of cervical cancer cells under illumination by a mechanism involving p53

High-risk Human Papillomaviruses (HPV) has been found to be associated with carcinomas of the cervix, penis, vulva/vagina, anus, mouth and oro-pharynx. As the main tumorigenic effects of the HPV have been attributed to the expression of E6 and E7 genes, different gene therapy approaches have been directed to block their expression such as antisense oligonucleotides (ASO), ribozymes and small interfering RNAs. In order to develop a gene-specific therapy for HPV-related cancers, we investigated a potential therapeutic strategy of gene silencing activated under illumination. Our aim according to this antisense therapy consisted in regulating the HPV16 E6 oncogene by using an E6-ASO derivatized with a polyazaaromatic ruthenium (Ru(II)) complex (E6-Ru-ASO) able, under visible illumination, to crosslink irreversibly the targeted sequence. We examined the effects of E6-Ru-ASO on the expression of E6 and on the cell growth of cervical cancer cells. We demonstrated using HPV16(+) SiHa cervical cancer cells that E6-Ru-ASO induces after illumination, a reactivation of p53, the most important target of E6, as well as the inhibition of cell proliferation with a selective repression of E6 at the protein level. These results suggest that E6-Ru ASOs, activated under illumination and specifically targeting E6, are capable of inhibiting HPV16(+) cervical cancer cell proliferation.

Photo-reactive Ru(II)-oligonucleotide conjugates: influence of an intercalating ligand on the inter- and intra-strand photo-ligation processes

The damaging efficacy towards OligoDeoxyriboNucleotides (ODNs) of two photoreactive polyazaaromatic ruthenium(II) complexes, Ru(T) and Ru(D), has been evaluated. Both compounds correspond to the known [Ru(TAP)(2)(dppz)](2+) complex, but they are anchored differently to a guanine-containing single strand ODN (probe strand). This has allowed us to investigate the influence of the interactions existing between the tethered complexes and the single or double strand, on the photo-ligation processes. From melting temperature measurements of the duplex formed between these Ru-ODNs and their complementary sequence (target strand), it has been found that Ru(T) anchored via the TAP ligand interacts with the duplex by means of the intercalating dppz ligand (head on geometry), while Ru(D) anchored via the dppz ligand likely adopts a side on geometry without intercalation. Both single stranded Ru conjugates self-inhibit in the absence of their target ODN by forming exclusively a cyclic "seppuku" photo-adduct (intra-molecular photoreaction). In contrast, this intra-molecular photo-product is precluded in presence of the target strand, and the Ru-ODN sequence photo-crosslinks with the latter (inter-molecular photoreaction). Both intra- and inter-molecular processes with both complexes are efficient (80% yields) and lead to stable photo-adducts. Interestingly, detailed studies have revealed that the similar photo-damaging efficacy of crosslinking by Ru(T) and Ru(D) is a consequence of a cascade of events with compensatory effects, originating from the different geometry of interaction of the tethered complexes. Notably, antagonistic effects are present when the complex is intercalated, the guanine oxidation step being highly favoured and the recombination of the quenching products being hindered.

Photo-cross-linking between polymers derivatized with photoreactive ruthenium-1,4,5,8-tetraazaphenanthrene complexes and guanine-containing oligonucleotides

We have shown previously that complexes containing 1,4,5,8-tetraazaphenanthrene (TAP) ligands are able to form photoadducts with the guanine bases of DNA and oligonucleotides. In this work, we have exploited this specific photoreaction for carrying out photo-cross-linkings between guanine-containing oligonucleotides (G-ODNs) and biodegradable polymers derivatized with the photoreactive Ru(II) compounds. The aim in the future is to use these polymer conjugates as vectorizing agents of the metallic compounds inside the cells. Thus, photooxidizing Ru(II) complexes such as [Ru(TAP)3]2+ and [Ru(TAP)2phen]2+ (phen = 1,10-phenanthroline) have been derivatized by an oxyamine function to attach them, via an oxime ether linkage, to a soluble 6 or 80 kDa poly-[N-(2-hydroxyethyl)-l-glutamine] polymer that contains pendent aldehyde groups. It is demonstrated that the resulting Ru-labeled polymers exhibit photophysical properties and a photochemistry that are comparable with those of the free, nonattached complexes. The photo-cross-linkings with the G-ODNs are clearly detected by gel electrophoresis with the 6 kDa Ru conjugates upon illumination.