A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA.

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

Synthesis of novel 2,8-disubstituted indolo[3,2-b]carbazoles.

A new synthetic pathway towards 2,8-difunctionalised indolo[3,2-b]carbazoles was investigated. The presented method offers a short and high yielding route towards 2,8-dibromo-5,11-dihexyl-6,12-diphenyl-indolo[3,2-b]carbazole. It is demonstrated that the latter compound is a versatile building block, enabling the synthesis of a number of previously unreported 5,11-dialkyl-6,12-diphenyl-indolo[3,2-b]carbazoles in moderate to good yields, using Suzuki and Sonogashira cross-coupling reaction. Furthermore it is shown that 2,8-dibromo-5,11-dihexyl-6,12-diphenyl-indolo[3,2-b]carbazole can be easily formylated, giving rise to the 2,8-diformyl-5,11-dihexyl-6,12-diphenyl-indolo-[3,2-b]carbazole. The latter compound was successfully subjected to condensation reactions.

Fluorescent SAM analogues for methyltransferase based DNA labeling.

In this work, the preparation of new S-adenosyl-l-methionine (SAM) analogues for sequence specific DNA labeling is evaluated. These non-natural analogues, comprising cysteine rather than the natural homolog, were obtained in near quantitative conversions from readily available starting materials without relying on using an excess amount of labor intensive molecules. The synthetic strategy was used to generate fluorescent cofactors, with colours spanning the whole visible spectrum, and their applicability in methyltransferase based optical mapping is shown.

A facile and general method for the synthesis of 6,12-diaryl-5,11-dihydroindolo[3,2-b]carbazoles.

A facile and general two-step method towards 6,12-diaryl-5,11-dihydroindolo[3,2-b]carbazoles has been developed. Hydroiodic acid was an efficient catalyst for the condensation of indole and aromatic aldehydes, and iodine was used as an oxidation reagent to afford symmetrical 6,12-diaryl-5,11-dihydroindolo[3,2-b]carbazoles in moderate to good overall yields.

Improved Spectral Coverage and Fluorescence Quenching in Donor-acceptor Systems Involving Indolo[3-2-b]carbazole and Boron-dipyrromethene or Diketopyrrolopyrrole.

A novel π-conjugated triad and a polymer incorporating indolo[3,2-b]-carbazole (ICZ) and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) were synthesized via a Sonogashira coupling. Compared to the parent BODIPY the absorption and fluorescence spectrum were for both compounds broader and redshifted. The redshift of the fluorescence and the decrease of the fluorescence quantum yield and decay time upon increasing solvent polarity were attributed to the formation of a partial charge-transfer state. Upon excitation in the ICZ absorption band the ICZ fluorescence was quenched in both compounds mainly due to energy transfer to the BODIPY moiety. In a similar ICZ-π-DPP polymer (where DPP is diketopyrrolopyrrole), a smaller redshift of the absorption and fluorescence spectra compared to the parent DPP was observed. A less efficient quenching of the ICZ fluorescence in the ICZ-π-DPP polymer could be related to the unfavorable orientation of the transition dipoles of ICZ and DPP. The rate constant for energy transfer was for all compounds an order of magnitude smaller than predicted by Förster theory. While in a solid film of the triad a further redshift of the absorption maximum of nearly 100 nm was observed, no such shift was observed for the ICZ-π-BODIPY polymer.

A highly sensitive, selective, colorimetric and near-infrared fluorescent turn-on chemosensor for Cu2+ based on BODIPY.

A new colorimetric and NIR fluorescent chemosensor (1) for Cu(2+) based on BODIPY is reported, displaying a highly sensitive and selective fluorescent enhancement with Cu(2+) among various metal ions, upon excitation at 620 nm in CH(3)CN.