mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo

Self-cleavage assays of RNA folding reveal that mRNA structures fold sequentially in vitro and in vivo, but exchange between adjacent structures is much faster in vivo than it is in vitro

Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping

Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58–156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes

Organonickel(IV) Chemistry: A New Catalyst?

With scorpionate ligands finding their way into organonickel chemistry, the state of the art of present-day nickel(IV) chemistry is highlighted. Will rapid CX coupling reactions emerge as a domain of higher-oxidation-state nickel chemistry

Bis(dimethylphosphino)methan-Nickel(0)-Komplexe

The reaction of tris(ethene)nickel(0) with stoichiometric amounts of bis(dimethylphosphino)methane (dmpm) in ether at low temperature affords the yellow crystalline, dinuclear complexes (dmpm)Ni2(CH4)4 (1) and (dmpm)2Ni2(C2H4)2 (2). 2 reacts with ethyne to yield (dmpm)2Ni2(C2H2)2 (3). When 2 is treated with CO at —40 °C the primary product is (dmpm)2Ni2(CO)2(µ-CO) (4). At 20 °C 4 is converted by additional CO into (dmpm)2Ni2(CO)4 (5), which has already been characterized as the reaction product of Ni(CO)4 with dmpm. In compounds 1—5 the bidentate dmpm acts as a bridging and not as a chelating ligand. The structures of complexes 1—4 were assigned on the basis of their 13C and 31P NMR spectra

Applying the Macrocyclic Effect to Smaller Ring Structures. N,N‘-Dimethyl-3,7-diazabicyclo[3.3.1]nonane Nickel(0) Complexes

The two N donor atoms in the tertiary diamine N,N‘-dimethyl-3,7-diazabicyclo[3.3.1]nonane (dabn, C9H18N9) are ideally positioned in the bicyclic structure for chelation to a metal center. This feature was utilized to synthesize unusual diamine nickel(0)−ethene and −ethyne complexes, which represent limiting cases of the Pearson hard-soft acid-base concept. Thus, the reaction of Ni(C2H4)3 with dabn affords yellow TP-3 (C9H18N2)Ni(C2H4) (1) (dec. 0 °C) in which the ethene ligand displays extreme high-field NMR shifts at δ(H) 0.27 and δ(C) 20.4 and an exceptionally small coupling constant 1J(CH) = 142 Hz. Reaction of 1 with butadiene yields the red mononuclear T-4 complex (C9H18N2)Ni(η2-C4H6)2 (2a) in solution, from which the dinuclear derivative {(C9H18N2)Ni(η2-C4H6)}2(μ-η2,η2-C4H6) (2) (dec. 20 °C) is isolated. Complexes 2 and 2a are more soluble than 1 and thus better suited for further reactions. When ethyne is added to a solution of 2 or 2a at −78 °C, the yellow TP-3 complex (C9H18N2)Ni(C2H2) (3) (dec. −30 °C) is obtained. The ethyne ligand of 3 exhibits the lowest IR C⋮C stretching frequency (1560 cm-1) and by far the smallest NMR coupling constant 1J(CH) = 178 Hz yet reported for a mononuclear nickel(0)−ethyne complex. In addition, Ni(CO)4 reacts with dabn to yield orange T-4 (C9H18N2)Ni(CO)2 (4). The results demonstrate that tertiary diamines, which are hard Lewis bases and which a priori are expected to coordinate poorly to the soft Lewis acid Ni(0), may be supported in such a coordination by the stabilizing principle of preorganization and consequently act as very powerful donor ligands

cis-(R‘₂PC₂H₄PR‘₂)PdH(SnR₃) Complexes: Trapped Intermediates in the Palladium-Catalyzed Hydrostannation of Alkynes

The complexes (R'2PC2H4PR'2)Pd(C2H4) (R' = iPr, tBu) react with R3SnH (R = Me, nBu) by displacement of the ethene ligand and oxidative addition of the Sn−H bond to generate the chelating phosphane stabilized cis PdII hydrido stannyl complexes (R'2PC2H4PR'2)PdH(SnR2) (R' = iPr (1), tBu (2)). Complex 1a (R' = iPr, R = Me), containing the smallest substituents, is only transiently formed but has been detected at −80 °C by NMR spectroscopy. It reacts further with Me3SnH, even at −120 °C, by eliminating hydrogen to give (dippe)Pd(SnMe3)2 (3). In contrast, the isolated (dippe)PdH(SnnBu3) (1b) is briefly stable at ambient temperature, whereas the sterically encumbered species (dtbpe)PdH(SnR3) (R = Me (2a), nBu (2b)) are stable well above 100 °C. The molecular structure of 2a has been determined by X-ray crystallography. Complex 2a reacts with 2 equiv of C2R''2 (R'' = CO2Me) to give (dtbpe)Pd(C2R''2) (4) and predominantly the corresponding (E)-vinylstannane (E)-(R'')(H)CC(SnMe3)(R'') (E-5). Since 2a also catalyzes the hydrostannation of the alkyne, the cis PdII hydrido stannyl complexes 1a,b and 2a,b represent trapped intermediates in the Pd-catalyzed hydrostannation of alkynes. The existence of the complexes also sheds light on the mechanism of the Pd-catalyzed degradation of R3SnH into Sn2R6 and H2

Degradation of Dichloromethane by Bispidine

An effective degradation reaction of CH2Cl2 by bispidine (3,7-diazabicyclo[3.3.1]nonane, C7H12(NH)2, 1) is reported. The reaction starts as low as -20?degrees C and is quantitative with respect to 1. The overall reaction implies nucleophilic substitution of chloride, followed by a series of cascading acidbase reactions, ending with the formation of two easily separable products, one being soluble and the other insoluble. The starting 1, the intermediates, and the products show a variety of interesting solid-state structures, associated with plasticity, NH?N and NH?Cl?HN hydrogen bonding, and polymorphism. Copyright (c) 2012 John Wiley & Sons, Ltd