Oligonucleotide Analogues with Integrated Bases and Backbone. Part 20

Abstract

Hydrazide-and amide-linked oligonucleoside analogues with integrated bases and backbone were designed to allow for a rapid synthesis of long and water-soluble oligomers. The uracil-, cytosine-, and adenine-derived hydrazide building blocks 13 -15 were synthesized by nucleophilic substitution with the hydrazine 23 of the halides 19, 28, and 34, derived from the alcohols 18, 27, and 33, respectively, while the uracil-, cytosine-, and adenine-derived amide building blocks 45 -47 were synthesized by a Curtius degradation of the carboxylic acids 51, 56, and 61. These acids were obtained by Wittig reaction of the aldehydes 49, 53, and 58. The guanine-derived monomers 44 and 48 were synthesized by reductive cyclisation of the nitroso amides 38 and 63, respectively, resulting from acylation of the known 2,6diamino-4-(benzyloxy)-5-nitrosopyrimidine (37).Stacking of the nucleobases and the right geometry for Watson -Crick base pairing required adjusting the torsion angles k, x, and z from À 50, 180, and À 90 to À 70, þ 70, and À 1008, respectively ( Fig. 1, b ! c). We assumed that changing k and z from their energetically ideal values will result in only little torsional strain, and that the energy to be paid would be overcompensated by the H-bonds between the nucleobases [11] [25], and by base stacking [26]. However, calculations 7 ) to evaluate the energy to be paid for the adjustment of the torsion angle x from 1808 to þ 708 gave contradictory results 8 ). It is thus not possible to specify an overall energy value to be paid for the conformational transition from conformer b to c in Fig. 1.Modelling studies of various dimers suggested that stacking interactions depend on the sequence, and decrease in the order UA % UU % AA > AU. To evaluate the formation of duplexes between longer oligonucleotide analogues, we minimised the conformational energy of the octamer U 4 A 4 (Fig. 3) 9 ). The model suggested Watson -Crick-type base pairing and base stacking, with the hydrazide linker adopting a conformation with torsion angles k -z as deduced for the cyclic duplex (Fig. 1, c). The Helvetica Chimica Acta -Vol. 92 (2009) 1138. Model of the hydrazide-linked octamer U 4 A 4 . a) Side view. b) Top view. 7 ) Ab initio calculations using Spartan 06 and the 6-31G* basis set. 8 ) The conformational energies of N-methyl-2-(6-methyluracil-1-yl-)acetamide and N-methyl-2-(8methyladenine-9-yl-)acetamide were minimised, resulting in an energy minimum of x ¼ À 708 (cf. experimentally favoured: x ¼ 1808). The value of x ¼ 708, required for duplex formation, corresponds to a calculated energy maximum. 9 ) Amber* force-field calculation using Macromodel 7.0, with the H-bonds between the nucleobases constrained.

Synthesis of alanyl nucleobase amino acids and their incorporation into proteins

“…CBz protection of cytosine afforded compound 1 in 74% yield. 12 Compound 1 underwent coupling with N -Boc-L-serine β-lactone in the presence of DBU to afford N-protected cytosyl amino acid derivative 2 in 56% yield. 11 Compound 2 was treated with SOCl 2 in methanol to form methyl ester 3 and then the CBz protecting group was removed by hydrogenolysis over Pd/C to afford 4 .…”

“…N -Pentenoyl protection of adenine afforded compound 18 , the latter of which underwent coupling with N -Boc-L-serine β-lactone to afford compound 19 in 43% yield. 11,12 Boc deprotection of N α and subsequent reprotection using 4-pentenoic acid succinimide ester in the presence of K 2 CO 3 afforded N -dipentenoyl amide 20 in 41% yield for two steps. 14 Free carboxylic acid 20 was activated as cyanomethyl ester 21 in 31% yield.…”

PNA‐Hybridsequenzen als Erkennungseinheiten in SNARE‐Protein‐analogen Peptiden

“…N4-Z-Cytosine was synthesized from cytosine as described in Ref. [9]. The conversion of the Boc-protected alanyl nucleo amino acids into the Fmoc-protected building blocks was performed as described in Ref.…”

Synthesis of the Fmoc-aza-Arg(Boc)2 precursor via hydrazine alkylation

“…* Corresponding author, anton.mastitski@ut.ee most cases these precursors have been prepared from carbonyl compounds via reductive alkylation of protected hydrazines [3][4][5] (Scheme 1, A). However, there are other synthetic routes, mainly based on alkylation of N′-mono-or di-substituted hydrazine derivatives with alkyl halides [4,[6][7][8] (Scheme 1, B), or introducing a protecting group into commercially available alkyl hydrazines [4,[7][8][9][10] (Scheme 1, C). However, in the case of some aza-amino acid precursors these straightforward synthetic routes cannot be used.…”