No abstract

The sodium hydride mediated cyclization of arylacetonitriles with oxalic acid bis(imidoyl) dichlorides, aza-analogues of oxalyl chloride, afforded functionalized 2-alkylidene-3-iminoindoles with very good regio- and E/Z selectivity. Excellent chemoselectivities were observed for functionalized substrates. Based on these results a domino "cyclization-lactamization" reaction of bis(imidoyl) chlorides with methyl 2-(cyanomethyl)benzoate was developed. This process allowed a convenient one-pot synthesis of indolo[1,2-b]isoquinolin-5-ones related to tryptanthrin. A new and convenient synthesis of delta-carbolines by intramolecular electrocyclization-elimination reactions of 2-alkylidene-3-iminoindoles was developed. It was shown that delta-carbolines selectively bind to triplex or duplex DNA (intercalation). Indirubine analogues were prepared by deprotection and lactonization of functionalized 2-alkylidene-3-iminoindoles.

A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.