3-Fluoro-2-mercuri-6-methylaniline Nucleotide as a High-Affinity Nucleobase-Specific Hybridization Probe

Abstract

A 3-fluoro-6-methylaniline nucleoside was synthesized and incorporated into an oligonucleotide, and its ability to form mercury-mediated base pairs was studied.UV melting experiments revealed increased duplex stability with thymine, guanine, and cytosine opposite to the probe and a clear nucleobase-specific binding preference (T > G > C > A). Moreover, the 3-fluoro group was utilized as a spin label that showed distinct 19 F NMR resonance shifts depending on the complementary nucleobase, providing more detailed information on Hg(II)-mediated base pairing.

1,8‐Dimercuri‐6‐Phenyl‐1H‐Carbazole as a Monofacial Dinuclear Organometallic Nucleobase

“…Previous studies with oligonucleotides incorporating coordinative or organometallic Hg II ‐mediated base pairs have revealed less negative enthalpies and entropies of hybridization compared to unmodified duplexes, consistent with dehydration of the bridging Hg II ion . However, the pattern observed with ON1 z and ON1 z‐Hg 2 was quite different.…”

“…Table summarizes the oligonucleotide sequences used in the present study. In the modified oligonucleotide ON1 z , the sequences flanking the central 6‐phenyl‐1 H ‐carbazole C ‐nucleoside were identical to those previously used in related studies on 5‐mercuricytosine and 2‐fluoro‐3‐mercuri‐6‐methylaniline, allowing direct comparison of the hybridization properties. 5‐Methylcytosine residues were used instead of cytosine residues to prevent off‐target mercuration.…”

“…[5] Previous studies with oligonucleotides incorporating coordinative or organometallic Hg II -mediatedb ase pairs have revealed less negative enthalpies and entropies of hybridization compared to unmodified duplexes, consistent with dehydration of the bridging Hg II ion. [9][10][11] However,t he pattern observed with ON1 z and ON1 z-Hg 2 was quite different.T he enthalpies( Table 2) and entropies (Table 3) of hybridizationw ere highly negative for all of the duplexess tudied and in most cases both values were more negative with ON1 z-Hg 2 than with ON1 z.O nly duplexes ON1 z·ON2 t and ON1 z-Hg 2 ·ON2 t Chem.E ur.J. 2020, 26,2164 -2168 www.chemeurj.org exhibitedt he "normal" pattern of less negative enthalpies and entropies of hybridization for the mercurated duplex and even in that case the difference wassmall.…”

Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA

“…Even though the T-Hg(II)-T pair is a paradigm of a metal-mediated base pair, examples for other Hg(II)-mediated base pair are scarce. The only other instances involve pyridine [61] or organometallic-mercurated ligands [62][63][64][65]. Hence, Hg(II)mediated base pairs formed from an artificial mispair are a rarity.…”

Covalently Mercurated Molecular Beacon for Discriminating the Canonical Nucleobases

“…Our related approach shows the potential to discriminate also purine nucleobases. For this purpose, we used a recently developed organometallic 3‐fluoro‐2‐mercuri‐6‐methylaniline nucleotide (F−Hg; Figure 1) because of promising results on discriminating natural nucleobases within double‐helical DNA by 19 F NMR and UV melting temperature measurements [8] . In the present article, the nucleoside analogue is part of the loop region of a molecular beacon.…”