Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2′-deoxy-5-propynylcytidine

Abstract

Non-branched and branched oligonucleotides incorporating consecutive runs of 2'-deoxy-5-propynylcytidine residues () instead of 2'-deoxycytidine () were synthesized. For this, phosphoramidite building blocks of 2'-deoxy-5-propynylcytidine () were prepared using acetyl, benzoyl or N,N-di-n-butylaminomethylidene protecting groups. The formation of the i-motif assemblies incorporating 2'-deoxy-5-propynylcytidine residues was confirmed by temperature-dependent CD- and UV-spectra as well as by ion-exchange chromatography. The low pK(a)-value of nucleoside (pK(a) = 3.3) compared to dC (pK(a) = 4.5) required strong acidic conditions for i-motif formation. Branched oligonucleotide residues with strands in a parallel orientation lead to a strong stabilization of the i-motif allowing aggregation even at non-optimal pH conditions (pH = 5). The immobilization of oligonucleotides incorporating multiple residues of on 15 nm gold nanoparticles generated DNA-gold nanoparticle conjugates which are able to aggregate into i-motif structures at pH 5.

Enzymatic Primer-Extension with Glycerol-Nucleoside Triphosphates on DNA Templates

“…The final purified products 1u and 1c were characterized by 1 H- and 31 P-NMR and by ESI-MS. In addition, 1u and 1c have similar UV absorption profiles to those reported for 5-propynyl-deoxyribonucleosides [15].…”

“…A di-butylaminomethylidene group was used to protect the exocyclic amine of 3c instead of an acetyl or benzoyl group in order to avoid a potential cyclization side-reaction involving the amide and the 5-propynyl group [14]. The presence of a propynyl group in 4u and 5c was confirmed by the characteristic chemical shift (4–5 ppm) of the methyl carbon in 13 C NMR [15] together with 1 H-NMR and ESI-MS analysis. gU prop TP and gC prop TP ( 1u and 1c ) were synthesized from the corresponding nucleosides ( 5u and 6c ) using the one-pot, salicylchlorophosphorin approach developed by Ludwig and Eckstein [16].…”

The effect of the glycosylation position on the base pairing and supramolecular structure of the 5′-deoxyribosyl Janus-type AT nucleosides

“…For purine nucleosides, the N7eH!N9eH transition can lead to the formation of N7 and N9 regioisomers in the case of the 2 0 -deoxyribonucleosides [13]. Except for these canonical nucleosides, other modified heterocyclic systems have been also shown to possess the same phenomena, such as the N8 and N9 pyrazolo [3,4-d]pyrimidine ribonucleoside analogs [14], as well as the N7, N8 and N9 triazolo [4,5-d]pyrimidine derivatives [15].…”

Ph-Dependent Assembly of DNA-Gold Nanoparticles Based on the i-Motif

“…For the synthesis of the branched oligonucleotide 7 a dendrimeric branching residue (Glen Research, USA) was used. [6] The oligonucleotides 1-3 were immobilized on the surface of 15 nm gold nanoparticles according to the procedure TABLE 1 Thiol-modified oligonucleotides 1-3 utilized for the immobilization on gold nanoparticles, DNA gold nanoparticle conjugates 4-6, and the branched oligonucleotide 7 described previously. [3] The resulting DNA gold nanoparticle conjugates 4-6 ( Table 1) …”