Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties

Abstract

Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular Hg -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than Hg -mediated base pairing.

Covalently Palladated Oligonucleotides Through Oxidative Addition of Pd0

“…Scheme2.Palladation of oligonucleotide ON1 b-I by oxidative addition.R eagents and conditions: Pd 2 (dba) 3 ,H 2 O, MeCN,Ara tmosphere,5 58C, 18 h.…”

“…[1] To widen the scope of the latter application to biological systems, that is, to overcome the scarcity of transition metals available for metal-mediated base pairingi nt he intracellular medium, we have explored the possibility of using oligonucleotides with organometallic nucleobase surrogates. [2,3] We have successfully synthesizeds uch structures by two approaches-eitherd irect mercuration of electron-richs ites on aromatic rings [4] or ligand-directed cyclopalladation of benzylamine or phenylpyridine moieties. [5] Palladationof aromatic rings withoutt he assistance of ad irecting ligand would also be desirable, as the resultingm onodentate organopalladium complexes wouldl eave the palladium center more exposed and amenable to pseudo-linear coordination (Figure 1).…”

Organomercury Nucleic Acids: Past, Present and Future

“…Flipping of a pyrimidine base from anti to syn conformation places its C5 in the position normally occupied by N3. Therefore, the C5-Hg II -N3-linked base pairs of 5-mercuricytosine [88] and 5-mercuriuracil [89] with thymine (Figure 2A and B) are in all likelihood isosteric with the well-documented N3-Hg II -N3-linked base pair between two thymines (Figure 2D). [72][73][74][75] A similar geometry seems likely also for the 3-fluoro-2-mercuri-6-meth-ylaniline-thymine base pair (Figure 2C).…”

Synthesis and Hybridization Properties of Covalently Mercurated and Palladated Oligonucleotides

“…The relatively electron-rich C5 carbons of cytosine and uracil bases are readily mercurated by Hg(II) salts under mild conditions (Scheme 1, A and B). 8,10,11 In an oligondeoxynucleotide, mercuration can be limited to the desired cytosine residues by using 5-methylcytosine in place of all the others. 10 Besides cytosine and uracil, artificial bases such as phenol 12 can also be mercurated by the same method provided that they are sufficiently electron-rich.…”

“…Our first experiments with triplex-forming oligonucleotides bearing a 3′-terminal 5-mercuricytosine residue indeed revealed increased Hoogsteen as well as Watson-Crick melting temperatures with A•T or T•A as the target base pair. 11 The origin of this stabilization remained obscure, however, as the effect was actually amplified in the presence of 2-mercaptoethanol, a strong competing ligand for Hg(II). 18…”