DNA functionalization by dynamic chemistry

Abstract

SummaryDynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

Template‐Directed Incorporation of Functional Molecules into DNA

“…In order to introduce commercially available d ‐threoninol into oligonucleotides, its corresponding phosphoramidite monomer ( 3 ) was synthesized (Scheme S1 in the Supporting Information) according to the procedures previously described in literature [16] . Phosphoramidite 3 was incorporated to the internal position of 13mer oligonucleotides applying automated solid‐phase synthesis (Table 1).…”

“…For this reason, four aldehyde‐bearing nucleobases ( G CHO , C CHO , A CHO and T CHO ) were added to the reaction along with phenanthroline. Aldehyde‐carrying nucleobases were synthesized according to the procedure previously described in the literature (see the structures in Supporting Information) [15,16] …”

“…Phosphoramidite monomer 1 [16] and aldehyde modified phenanthroline ( P CHO ) [19] were prepared according to published procedures. Oligonucleotides were synthesized on DNA/RNA/LNA Synthesizer (K&A Laborgeräte, Schaafheim, Germany) using standard phosphoramidite method.…”

“…[15] Inspired from Ghadiri's work, in our previous study, we used imine exchange reaction for reversible attachment of aldehyde carrying nucleobase monomers on to DNA oligonucleotides with an acyclic threoninol backbone. [16] The addition of a complementary DNA template into the reaction condition increased the selection of the specific nucleobase among all four nucleobases. This complementary nucleobase of the template directed the incorporation of the right nucleobase through base pairing.…”

Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily‐Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3

“…Currently,f ew methods have been reported for the analysis of single-templated DCC, [8,19] these include HPLC analysis; [20,21] NMR spectroscopy studies; [22][23][24] X-ray crystallography; [25] sizeexclusion chromatography (SEC); [26,27] and, more recently,t he use of polymer-scaffolded (PS-DCLs), [28] DNA, [29][30][31][32] or peptide nucleic acid (PNA)-encoded [33,34] dynamic combinatorial libraries (DCLs). However,t hesem ethods only detect amplification of the bestb inders in the presence of the template, and cannotd istinguish which templatei sr esponsible for the ob-served amplification;h ence they are unsuitable for the proposed multiprotein DCC system.…”