Oligonucleotides Featuring a Covalently Mercurated 6‐Phenylcarbazole Residue as High‐Affinity Hybridization Probes for Thiopyrimidine‐Containing Sequences

Abstract

Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2-or 4thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2-and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear Hg II -mediated base pairs featured a coordinated covalent bond between Hg II and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear Hg II -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one Hg II ion coordinated to a thio and the other one to an oxo substituent.

Organometallic modification confers oligonucleotides new functionalities

“…Initially, these studies were motivated by the desire to enhance the hybridization affinity of therapeutic oligonucleotides through metal coordination. Increased melting temperatures have indeed been observed for many short double- 105,108,110,125,127,149–151 and triple-helical 123,147 oligonucleotides incorporating a single organometallic residue and in one case a palladacyclic splice-switching oligonucleotide modestly outperformed its unmodified counterpart in a human cell line. 152 The connection between these two observations, however, remains uncertain.…”

“…As higher hybridization affinity often comes at the cost of lower sequence selectivity, we were surprised to find that in some cases an organometallic nucleobase surrogate not only increased the melting temperature of a double helix but also robustly discriminated between canonical nucleobases. 110,125,127 Inspired by these results, the focus of our studies on oligonucleotides bearing organometallic base modifications has recently been on potential applications in single nucleotide polymorphism (SNP) genotyping. 153…”

“…2(D) and (E)) so it was not unexpected to once again observe a similar pattern of hybridization preferences for the corresponding modified oligonucleotide. 125 Curiously, switching the Hg( ii ) from C1 to C8 had no effect on pairing with guanine or thymine but pairing with adenine and cytosine became much more favorable. The most interesting results, however, were obtained with duplexes placing either 2- or 4-thiothymine opposite to the organometallic residue.…”

“…104 Some artificial nucleobase analogues 110 are much more reactive than the natural pyrimidine bases but even so cytosines should be replaced by 5-methylcytosines and uracils by thymines to prevent off-target mercuration. This approach has been successful with short oligonucleotides 105,110,123–127 but has never been tested with very long ones.…”

Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation

“…The use of these artificial nucleosides enables a fine-tuning of the metal-binding abilities of the nucleic acids, thereby enabling the development of different applications. A more recently reported use of nucleic acids with metal-mediated base pairs involves improved strand displacement reactions, metal-responsive DNAzymes, , responsive nucleic acids in general, hybridization probes, − modulation of aptamer function, and the generation of DNA-templated silver nanoclusters . In addition, contiguous metal-mediated base pairs are currently under investigation in the context of generating one-dimensional arrays of metal ions − with potential applicability as conducting DNA nanowires. , …”