Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

Background: The translation or stability of the mRNAs from ferritin, m-aconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of higher-solution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.Results: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.Conclusions: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes, The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.     

Epoxide-opening and group-transfer reactions mediated by monomeric zirconium imido complexes

N-tert-Butylimidozirconocene (Cp2Zr=Nt-Bu) and its analogue (ebthi)Zr=NAr (ebthi = ethylenebis(tetrahydroindenyl), Ar = 2,6-dimethylphenyl) undergo overall cycloaddition reactions at ambient temperature with epoxides that lack accessible beta-hydrogens. The process results in addition of the Zr=N bond to an epoxide C-O bond, leading to azazirconacyclopentanes. The regio- and stereochemistry of the products implicate a stepwise mechanism, with the intermediacy of zwitterions having substantial carbocation character at the substituted carbon of the ring-opened epoxide-derived fragment. The azametallacycles undergo facile cleavage to beta-amino alcohols upon addition of mild acid.     

Synthesis of some 4-carboxy-3- and 5-(2-hydroxyalkyl)pyrazole lactone derivatives

The synthesis and biological activities of some 4-oxo-1-or-2-substituted 1H-or-2H-pyrano[4,3-c]pyrazole derivatives are described.     

Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan

The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.     

A Short,Affordable, One-Pot Synthesis of a Camphor-Derived Amino Alcohol

The commercially available α-ketoxime of camphorquinone (1) was reduced to the corresponding exo,exo-amino alcohol (2) in a two-step, one-pot procedure using sodium borohydride and nickel(II) chloride hexahydrate.     

Thermodynamic analysis of receptors based on guanidinium/boronic acid groups for the complexation of carboxylates, alpha-hydroxycarboxylates, and diols: driving force for binding and cooperativity

The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.     

Thermal‐ and Light‐Induced Spin Crossover in a Guest‐Dependent Dinuclear Iron(II) System

We previously reported the dinuclear material [Fe^II₂(ddpp)₂(NCS)₄] ? 4 CH₂Cl₂ ( 1? 4 CH₂Cl₂; ddpp=2,5‐di(2′,2′′‐dipyridylamino)pyridine) and its partially desolvated analogue ( 1? CH₂Cl₂), which undergo two‐ and one‐step spin‐crossover (SCO) transitions, respectively. Here, we manipulate the type and degree of solvation in this system and find that either a one‐ or two‐step spin transition can be specifically targeted. The chloroform clathrate 1? 4 CHCl₃ undergoes a relatively abrupt one‐step SCO, in which the two equivalent Fe^II sites within the dinuclear molecule crossover simultaneously. Partial desolvation of 1? 4 CHCl₃ to form 1? 3 CHCl₃ and 1? CHCl₃ occurs through single‐crystal‐to‐single‐crystal processes (monoclinic C2/c to P2₁/n to P2₁/n) in which the two equivalent Fe^II sites become inequivalent sites within the dinuclear molecule of each phase. Both 1? 3 CHCl₃ and 1? CHCl₃ undergo one‐step spin transitions, with the former having a significantly higher SCO temperature than 1? 4 CHCl₃ and the latter, and each has a broader SCO transition than 1? 4 CHCl₃, attributable to the overlap of two SCO steps in each case. Further magnetic manipulation can be carried out on these materials through reversibly resolvating the partially desolvated material with chloroform to produce the original one‐step SCO, or with dichloromethane to produce a two‐step SCO reminiscent of that seen for 1? 4 CH₂Cl₂. Furthermore, we investigate the light‐induced excited spin state trapping (LIESST) effect on 1? 4 CH₂Cl₂ and 1? CH₂Cl₂ and observe partial LIESST activity for the former and no activity for the latter.     

A Nanoscale Molecular Switch Triggered by Thermal,Light, and Guest Perturbation

Bottoms up! A discrete metallo‐supramolecular nanoball (see picture), synthesized by using “bottom‐up” methodologies, uniquely undergoes a solvent‐sensitive, physically addressable electronic spin switching. The switching occurs by thermal, light, or solvent perturbation, where importantly it can be switched “on” or “off” by green or red laser irradiation, respectively.