Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo.

We report on gas-phase experimental and theoretical studies on the neutral form of the green-fluorescent protein (GFP) chromophore using six different models, each carrying a spectator positive charge. Theoretical studies were carried out to quantify the effect of the spectator charge on the absorption maximum of the true neutral. The study also includes models having the possibility of forming intra-molecular hydrogen bonds, and their effect on the absorption profile is analyzed. The charge redistribution caused by a strong intra-molecular hydrogen bond was found to give rise to a red shift in going from non-hydrogen bonded to hydrogen bonded models. For the non-hydrogen bonded models, the length of the side chain as well as the group carrying the spectator charge, was varied to explore the possibility of shifts in absorption maximum due to these variations. No shifts were observed. The implications of these results in tuning the absorption maximum of the neutral form of the GFP chromophores are discussed.

Experimental evidence for a kinetic transition in reversible reactions.

We provide a first experimental verification of a theoretical prediction of a kinetic transition in a reversible binding reaction, AB right harpoon over left harpoon A+B, driven by the difference in effective lifetimes of the bound and the unbound states. We consider the kinetics of excited-state proton transfer to solvent from a photoacid whose conjugate anionic base possesses an extremely short unbound anion lifetime. Its solvent variation relative to the overall dissociation rate coefficient induces a transition in the kinetics, from power law to exponential.

Role of hydrophobic effects in the reaction of a polynuclear aromatic diol epoxide with oligodeoxynucleotides in aqueous solutions.

The need for large-scale direct synthesis of stereochemically defined and site-specific benzo[alpha]pyrenediol epoxide-oligodeoxyribonucleotide adducts for detailed NMR and other biochemical and physicochemical studies has necessitated a better understanding of variables that lead to an enhancement of the reaction yields. It is shown that, in aqueous solution, the formation of noncovalent hydrophobic complexes between 7r, 8t-dihydroxy-9t,10t-epoxy-7,8,9,10-tetrahydrobenzo[alpha] pyrene (BPDE) and the single-stranded oligonucleotide 5'-d(CCATCGCTACC) precedes the covalent binding reaction of BPDE with the single deoxyguanosine residue. The yield of covalent reaction products (involving reaction of BPDE at the C10 position with the exocyclic amino group of the dG residue) increases with increasing DNA concentration and tends toward saturation at oligonucleotide single-strand concentrations above approximately 3 mM. The addition of NaCl (0.3 M) also tends to enhance the adduct reaction yields. However, organic solvents such as tetrahydrofuran in the reaction mixtures (10-40%) decrease the stabilities of the noncovalent complexes, which in turn leads to reductions in the yields of covalent BPDE-dG oligonucleotide adducts. The efficiencies of formation of hydrophobic complexes were probed by fluorescence and UV absorption techniques using the BPDE tetrol hydrolysis product 7,8,9,10-tetrahydroxytetrahydrobenzo[alpha]pyrene as a model system.