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Eudistomin U is a member of the β-carboline class of heterocyclic amine-containing molecules that are capable of binding to DNA. The structure of eudistomin U is unique since it contains an indole ring at the 1-position of the pyridine ring. While simple β-carbolines are reported to intercalate DNA, an examination of the mode of binding of eudistomin U has been lacking. We report preliminary spectroscopic (UV-Vis, thermal denaturation, CD) and calorimetric (DSC) data on the binding of eudistomin U to DNA, which suggest that eudistomin U binds weakly according to a mechanism that is more complicated than other members of its class.

Surface plasmon resonance (SPR) has been used extensively in the field of DNA/DNA, DNA/protein, and small molecule protein/DNA interactions. However, there have been growing concerns with regard to the proper designing of experiments and the quality of analysis and reporting of SPR results. Here we describe a protocol that is designed to address some of those issues. It encompasses procedural steps beginning with immobilization of streptavidin on CM5 chips to the final step of data reporting on DNA-polymerase interaction binding kinetics. In evaluating the protocol, we carried out experiments using a simple methodology developed in our laboratory, taking advantage of the high sensitivity and superior signal-to-noise ratio of Biacore T200. We probed the binary and ternary binding affinities between exonuclease-deficient Klenow fragment (Kf-exo-) and various arylamine DNA lesions. We employed unmodified and carcinogen-modified oligonucleotides in the presence and absence of dNTPs. The total time required to carry out the method to completion is between one and two weeks, approximately two days for the SPR binding assays and one week for synthesis, purification, and characterization of modified oligonucleotides. Though the protocol presented here is meant for Biacore T100 or T200 model, the overall methodology can be applied for other instruments also. Reagents

The title compounds 13, 14, 19, and 20 were prepared from 2-(6-carbethoxyhexyl)cyclopent-2-en-l-one (1). Conjugate addition of nitromethane and subsequent stereoselective reduction of the ketone 2 with lithium tri-sec-butyl hydride provided the desired natural prostaglandin stereochemistry on the five-membered ring. Protection of the hydroxyl group and ozonolysis of the nitronate salt gave the aldehyde 7 of the same stereochemistry. Unfortunately, condensation of this aldehyde with n-hexylamine and in situ NaBH4 reduction resulted in epimerization of the lower side chain and loss of stereochemical control. However, the natural prostaglandin stereochemistry could be retained by first reducing the nitro group, before proceeding with condensation (hexanal) and metal hydride reduction. Stereochemical assignments were in part established through intramolecular Condensation of the crude -trans and ß-trans siloxy aldehydes 7 and 8 with n-hexylamine was essentially complete in 4-6 h as judged by TLC. Surprisingly, TLC