Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.

A three-component photoreversible tag for thiols.

[structure: see text] A one-pot coupling of a 1,3-diketone, an aldehyde, and an alkanethiol has been developed to produce a protected sulfide. Through use of an o-nitrophenylbenzaldehyde, this method provides a one-step route to a photochemically reversible thiol-protecting group. The kinetics of photolysis were established using (1)H NMR analysis, which allows for the rate to be based on the entire reaction scheme.

In vivo reporter labeling of proteins via metabolic delivery of coenzyme A analogues.

We demonstrate site-specific reporter labeling of proteins within live cells. By accessing the coenzyme A (CoA) metabolic pathway with a cell-permeable pantetheine analogue, we deliver CoA-bound reporter molecules for post-translational protein modification in vivo. These methods may be applied to natural product pathway manipulation as well as applications in conventional molecular and cellular biology.