Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3′ double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3′ dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3′ double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for 3′ single terminal overhangs adjacent to a UA pair are also presented.

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An alternative synthesis of the lipophilic antifolate piritrexim (1) is outlined. Starting from ketone 2, treatment with phosphorus oxychloride and dimethylformamide gave the β‐chlorocrotonaldehydes 3E/Z, which were reacted with cyanoacetamide (6) in the presence of sodium hydride to yield a 3‐cyano‐2‐pyridone derivative 7. Chlorination of 7 with thionyl chloride and subsequent reaction with guanidine (9) gave rise to piritrexim (1). The reaction of β‐chlorocrotonaldehydes 3E/Z, with 2,4,6‐triaminopyrimidine (4) yielded iso‐piritrexim (5).

Two strategies towards the synthesis of Iso-Piritrexim (12) are described. A) The Mannich-reaction of ketone 2 yields the bases 4-HCl and 5-HCl. By means of LC base 4 is separated and treated with in situ generated 3,3-diaminoacrylonitrile (9) to yield the 2-aminonicotinonitrile 11. The cyclocondensation of 11 with guanidine provides Iso-PTX (12). B) Reduction and oxidation of the beta-ketoester 15 leads to the beta-ketoaldehyde 17, which is cyclocondensed with 2,4,6-triaminopyrimidine (18) to yield Iso-PTX (12). In the NCl-tumor-test Iso-PTX (12) shows a moderate activity against some leukemia and lung cancer cell lines.

gations. -Four structural analogues of piritrexim (VIa), i.e (VIb), (XII) and (XIII), are synthesized and evaluated for their antitumor activity against a panel of 60 human cancer cell lines. Compounds (VIb), (XIIa) and (XIII) show antitumor activities. -(ZINK, M.; LANIG, H.; TROSCHUETZ*, R.; Eur.