Nucleic Acid Template-Directed Assembly of Metallosalen−DNA Conjugates

Abstract

Watson-Crick base pairing organizes DNA duplex formation necessary for genetic information storage in biological systems. DNA and RNA templates also direct the specific binding of nucleotide substrates during diverse enzyme-catalyzed reactions in replication, transcription, and DNA repair pathways. Recently, nucleic acid recognition properties have been extended to nonbiological systems, where DNA base pairing has been used to drive the template-directed chemical ligation of oligonucleotides, 1 and the assembly of nanostructures and novel materials. 2 We have been interested in expanding the versatility of nucleic acid base pairing for the addressable synthesis of bioconjugates in aqueous solution. Metallosalen-DNA (4, Scheme 1) represents an ideal system to demonstrate the concept of nucleic acid template-directed molecular synthesis. Salens, which are constructed from two salicylaldehydes and a diamine, serve as ligands for a broad range of metal ions. Many metallosalens are compatible with aqueous conditions 3 and have demonstrated utility as DNA cleavage reagents 4 and versatile catalysts for enantioselective transformations. 3a,5 Template-directed synthesis of metallosalen-DNA conjugates offers a unique approach to a new class of metal-DNA hybrids. Metal-DNA conjugates previously have been employed as probes of DNA structure and electron transfer, 6 "chemical nucleases" for targeted nucleic acid cleavage, 7 and scaffolds for metal-mediated base pairing motifs. 8 Thus, metallosalen-DNA may offer a new bioconjugate platform for DNAorganized materials, nucleic acid cleavage and detection strategies, and in vitro evolution of novel ribozymes and deoxyribozymes. 9 Our approach to template-directed synthesis of metallosalen-DNA is illustrated in Scheme 1. The DNA-metallosalen building blocks consist of two DNA oligonucleotides modified, at either the 3′ or 5′ end, with salicylaldehyde moieties (1 and 2). The modified strands are aligned on a complementary nucleic acid template (3), bringing the salicylaldehyde groups into proximity in a duplex. The metallosalen conjugate then is assembled by addition of an appropriate metal and diamine. Herein we report the efficient DNA and RNA template-directed synthesis and characterization of purified metallosalen-DNA conjugates.A salicylaldehyde phosphoramidite (8, Scheme 2) was synthesized as a precursor to salicylaldehyde-DNA conjugates 1 and 2, necessary for metallosalen-DNA assembly. The protecting groups for 8, including a benzoate ester for the phenol and a 1,3-dioxane for the aldehyde, were chosen for their compatibility with DNA synthesis and postsynthetic deprotection. Starting from known salicylaldehyde derivative 5, 10 dioxane 6 was prepared by alumina-catalyzed acetalization. Direct benzoylation of 6 with benzoyl chloride afforded 7, which was converted to phosphoramidite 8 by standard methods. 11 Oligonucleotide 2 was synthesized by DNA phosphoramidite chemistry (3′-to-5′), using 8 in the final coupling step. Oligonucleotide 1, bearing a 3′-terminal salicylaldehy...

DNA–Metal Base Pairs

“…[21,22] A different strategy, developed by Sheppard et al, used the sequence-specific formation of DNA double strands to template the formation of metal complexes between ligands bound to the terminal phosphates of two single strands bound to the template. [23,24] Gothelf et al equipped linear or tripodal nanoscale building blocks with oligonucleotides as recognition sequences for the specific build-up of large aggregates, which were finally connected by metal complexes.…”

The Lock is the Key: Development of Novel Drugs through Receptor Based Combinatorial Chemistry

“…16). [137][138][139][140] Experiments were carried out at 37 °C at pH 7.0 with equimolar concentrations of one azide, one alkyne and DNA duplex A (1 μM). When any pair of hairpin polyamides (42a + 43a, 42a + 43b, 42b + 43a, 42b + 43b) was combined in solution, HPLC analysis of the reaction mixtures (verified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry) revealed significant acceleration of formation of hairpin dimers in the presence of DNA template with respect to the nontemplated reaction between 42a and 43a.…”

Homogeneous DNA-detection Based on the Non-enzymatic Reactions Promoted by Target DNA

“…[23][24][25][26][27][28][29][30][31][32][33][34] They are divided roughly into two groups, metal ion-mediated ligand (probe) modification [23][24][25][26][27][28] and base pairing. [29][30][31][32][33][34] These studies triggered their analytical applications.…”

“…After the first report of ligation that does not depend on the enzyme, 43 several research groups have been engaged in gene detection using ligation based on a variety of chemical reactions. 28,[44][45][46][47][48][49][50][51] Xu and Kool reported chemical ligation through nucleophilic substitution with high sequence fidelity. 44 They applied this techniques to a multiplex analysis of SNPs using FRET between the fluorescent dyes appended to the probes.…”