Mechanically manipulating the DNA threading intercalation rate

The dumbbell shaped binuclear ruthenium complex DeltaDelta-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur.     

Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

Synthesis of novel cyclic α-amino acid derivatives via a one-pot sequential Petasis reaction/palladium catalysed process

A novel one pot Petasis reaction/palladium catalysed process is described involving 2-iodo/bromo benzylamine, ethyl glyoxalate and aryl/heteroaryl boronic acids. The in situ generated carbinolamine/imine undergoes the Petasis reaction to afford 2 which reacts with carbon monoxide or allene (1 atm) in the presence of Pd(0) to generate acyl palladium or π-allyl palladium species which are intercepted intramolecularly by the proximal secondary amine to afford isoindolone/4-methylene-3,4-dihydroisoquinoline α-amino acid derivatives in good yield.     

Pd(0) catalyzed three-five-component C-2-arylallylation of active methylene heterocycles: pyrazolones, oxazolones, isoxazolones and N,N′-dimethylbarbituric acid

A Pd(0) catalyzed three-five-component cascade involving an aryl iodide, allene and a heterocyclic pronucleophile is used to prepare 2-arylallyl derivatives (10-12 and 16-24) from 3-phenyl-5-isoxazolone (6) and 1-phenyl-3-methylpyrazolin-5-one (7) in moderate yield. Similar cascade allylation of masked amino acids 4-methyl-2-phenyl-4H-oxazol-5-one (8a), 4-benzyl-2-phenyl-4H-oxazol-5-one (8b) and 4-isopropyl-2-phenyl-4H-oxazol-5-one (8c) gave analogous products (25-37) in good yield. N,N-Dimethylbarbiturates (38-49) are similarly prepared from N,N-dimethylbarbituric acid (9) in excellent yield.     

The role of optimization in some recent advances in data-driven decision-making

Mathematical Programming - In this paper, we present a new framework of bi-level unconstrained minimization for development of accelerated methods in Convex Programming. These methods use...