Following molecular transitions with single residue spatial and millisecond time resolution.

"Footprinting" describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions, respectively. The hydroxyl radical (*OH) is a uniquely insightful footprinting probe by virtue of it being among the most reactive chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved *OH footprinting is presented based on the Fenton reaction, Fe(II) + H(2)O(2) --> Fe(III) + *OH + OH(-). It is implemented using a standard three-syringe quench-flow mixer. The utility of this method is demonstrated by its application to the studies on RNA folding. Its applicability to a broad range of biological questions involving the function of DNA, RNA, and proteins is discussed.

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins.

'Footprinting' describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (*OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved .OH footprinting has been developed based on the Fenton reaction, Fe(II) + H2O2 --> Fe(III) + *OH + OH-. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function.

Deoxygenation of Polynuclear Metal-Oxo Anions: Synthesis, Structure, and Reactivity of the Condensed Polyoxoanion [(C(4)H(9))(4)N](4)(NbW(5)O(18))(2)O.

The deoxygenation of the mixed-metal polyoxoanion [(C(4)H(9))(4)N](3)NbW(5)O(19) with benzoyl chloride in dichloromethane forms quantitatively the condensed polyoxanion [(C(4)H(9))(4)N](4)(NbW(5)O(18))(2)O, in which two polyoxoanion fragments are linked together by a Nb-O-Nb oxo bridge. The product is characterized by a strong IR band at 692 cm(-)(1) assigned to a Nb-O-Nb stretch and a broad single (93)Nb NMR resonance at 975 ppm. Partial hydrolysis of [(C(4)H(9))(4)N](4)(NbW(5)O(18))(2)O to NbW(5)O(19)O(3)(-) in wet acetonitrile was observed by IR and (17)O NMR spectroscopy. The reaction of [(C(4)H(9))(4)N](4)(NbW(5)O(18))(2)O with a variety of alcohols and phenol forms alkoxide-derivatized polyoxoanions [(C(4)H(9))(4)N](2)Nb(OR)W(5)O(18) (R = methyl, ethyl, isopropyl, cholesteryl, phenyl). The similarity of the IR spectra of these deriviatives suggests that functionalization occurs at the terminal NbO oxygen. A crystallographic study of [(C(4)H(9))(4)N](4)(NbW(5)O(18))(2)O revealed a crystallographically imposed linear Nb-O-Nb oxo bridge (Nb-O(bridge) = 1.887(3) Å) and a structure in which the terminal tungsten-oxo bonds on the adjoining polyoxoanion fragments are eclipsed. Crystal data: orthorhombic, Cmca; Z = 4, a = 15.817(2) Å, b = 17.870(2) Å, c = 35.058(2) Å; V = 9928.0(10) Å(3); R = 5.52%.