Synthesis and triplex forming properties of pyrrolidino pseudoisocytidine containing oligodeoxynucleotides

Abstract

Pyrrolidino pseudo-C-nucleosides are isosteres of natural deoxynucleosides which are protonated at the pyrrolidino ring nitrogen under physiological conditions. As constituents of a triplex forming oligodeoxynucleotide (TFO), the positive charge is expected to stabilise DNA triple helices via electrostatic interactions with the phosphodiester backbone of the target DNA. We describe the synthesis of the pyrrolidino isocytidine pseudonucleoside and the corresponding phosphoramidite building block and its incorporation into TFOs. Such TFOs show substantially increased DNA affinity compared to unmodified oligodeoxynucleotides. The increase in affinity is shown to be due to the positive charge at the pyrrolidino subunit.

Synthesis of 5‐/8‐Halogenated or Ethynylated Lipophilic Nucleobases as Potential Synthetic Intermediates for Supramolec­ular Chemistry

“…Column chromatography was carried out on silica gel Merck-60 Compounds G8Alk10, G9Alk10 and G3Bn2 were not isolated. The synthesis and characterization of compounds 5-iodocytosine C3, [40] 5-iodoisocytosine iC3, [19] guanine G13, [33] 3,5-bis(dodecyloxy)benzyl chloride, [41] and 3,4,5-tris(dodecyloxy)benzyl bromide [42] has been reported elsewhere.…”

“…The nonnatural isocytosine analog iCAlk2 was also prepared following the halogenation-alkylation sequence. In this case, iodination was carried out in the presence of N-iodosuccinimide (NIS), [19] since it afforded better results than other methods. Alkylation was then performed using the same procedure as with the cytosine derivatives.…”

“…C NMR (75 MHz, DMSO-d6): δ = 160. 8, 150.7, 150.0, 67.5, 49.1, 31.7, 29.3, 29.2, 29.1, 29.00, 28.96, 26 9, 149.8, 148.1, 98.7, 82.1, 74.5, 49.4, 31.2, 29.0, 26.0, 22.4, 13.9 [19] Isocytosine (1.0 g, 9.0 mmol) was suspended in a 1:1 AcOH/H2O mixture (35 mL). The reaction mixture was stirred at 50 ºC for 15 minutes.…”

Tuning Molecular Recognition of RNA and DNA via Sugar Modification

“…We therefore prepared the corresponding pyrrolidinopseudonucleosides and incorporated them into oligonucleotides. TFOs containing pyrrolidino pseudoisocytidine units (dpψiC-series) exhibit a significant increase in triplex stability compared to unmodified TFOs in at least two different sequence contexts [14]. By comparison with TFOs containing ribo-pseudo-isoC units (drψiC-series) it clearly emerges that the increase in stability is associated with the protonation of the pyrrolidino ring nitrogen which confirms the presence of attractive electrostatic interactions between the additional positive charge in the TFOs and the phosphodiester backbone of the target duplex.…”

Highly Stable Pyrimidine‐Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue

“…[8c, [19][20][21] Moreover, in contrast with the fully modified BNA-TFOs, which are too rigid in the overall structure, [5b, 22] the 2',4'-BNA NC -modified TFOs, bearing a six-membered bridged structure like ENA, might pose suitable conformational flexibility in their overall structure, which facilitates stable triplex formation as well. The above facts are the reason for which the 2',4'-BNA NC -modified TFOs act as excellent TFOs for the recognition of the homopurinehomopyrimidine tract of dsDNA.…”