The preparation of 8-substituted guanines using a new phosphorus(III)-mediated cyclisation of 4-acylamino-5-nitrosopyrimidines as the key step is described.

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.

Purine derivatives Purine derivatives R 0540An Improved Procedure for the Preparation of 8-Substituted Guanines. -A variety of novel 8-substituted guanines (V) are synthesized via phosphorus(III)-mediated cyclization of readily available 4-acylamino-5-nitrosopyrimidines (III). -(XU, M.; DE GIACOMO, F.; PATERSON, D. E.; GEORGE, T. G.; VASELLA*, A.; Chem. Commun. (Cambridge) 2003, 12, 1452-1453; Lab. Org. Chem., ETH-Hoenggerberg, CH-8093 Zuerich, Switz.; Eng.) -M. Kowall 40-161

The protected hydrazide-linked uracil-and adenine-derived tetranucleoside analogues 17, 19, and 21 were synthesized in solution by coupling the dimeric hydrazines 6 and 10 with the carboxylic acids 7, 11, and 16. These hydrazines and acids were obtained by partially deprotecting the hydrazines 5, 9, and 15, and these were prepared by coupling the hydrazines 3 and 14 with the carboxylic acids 4 and 8. The crystal structure analysis of the fully protected UU dimer 5 showed the formation of an antiparallel cyclic duplex with the uracil units H-bonded via HÀN(3) and O¼C(2). Stacking interactions were observed between the uracil units with a buckle twist of 30.98, and between the uracil unit II and the fluoren-9-yl group of Fmoc (¼ 9H-fluoren-9-yl)methoxycarbonyl). The hydrazide HÀN(3') and the C¼O group of Fmoc form an intramolecular H-bond. The uracil-and adenine-derived, water-soluble hydrazide-linked selfcomplementary octamers 23 -32 and the non-self-complementary uracil derived decamer 33 were obtained by coupling the carboxylic acids 4 and 8 on a solid support. 1 H-NMR Analysis in CDCl 3 , mixtures of CDCl 3 and (D 6 )DMSO, and (D 8 )THF showed that the partially deprotected dimers 5, 6, 12, and 13 form weakly associated linear duplexes. The partially deprotected tetramers 17 and 18 do not associate. The hydrazide-linked octamers 23 -32 do not stack in aqueous solution, and the non-selfcomplementary decamer 33 does not stack with the complementary strands of DNA 43 and RNA 42. The Cbz-protected amide-linked octamers 51 -56 derived from uracil, adenine, cytosine, and guanine were obtained as the main products by solid-phase synthesis from the carboxylic acids 46 -49. The fully deprotected amide-linked octamers proved insoluble, and could neither be purified nor analysed. of peptide nucleic acids (PNAs), the synthesis of the higher oligomers could follow either a Boc- [15] or an Fmoc-based [16] strategy; we opted for the Fmoc strategy that allows for deprotection under milder conditions.The synthesis in solution should lead to sufficient amounts of di-and tetramers to analyse their association in organic solvents by 1 H-NMR spectroscopy, as described for earlier types of ONIBs [4] [8] [9] [17]. Much smaller amounts of material are obtained by synthesis on solid support, and the association of the self-complementary octamers in aqueous solution has to be analysed on the basis of their temperature-dependent UV spectra [18] to assess p-stacking, the major stabilising force in aqueous solvents [19]. We also intended to test for cross-pairing of a non-self complementary hydrazidelinked decamer with complementary strands of RNA and DNA.We already reported the synthesis of the required monomeric building blocks [2], and now describe the synthesis of uracil-and adenine-derived, hydrazide-linked di-, tetra-, octa-, and decamers and of amide-linked octamers.