Generation of multicolored,prestained molecular weight markers for gel electrophoresis

Molecular weight marker proteins are routinely used in sodium dodecyl sulfate-polyacrylamide gel electrophoresis to estimate the relative molecular mass of specific proteins within a sample. This report describes a simple procedure for the generation of multicolored molecular weight proteins using a variety of Remazol-reactive textile dyes. These multicolored proteins provide a set of unambiguous markers for gel electrophoresis. Furthermore, the colored markers can be used in conjunction with Western blotting techniques to provide a visual display of marker proteins on the transfer membrane.     

The contact process on finite homogeneous trees

Let ? _d be a homogeneous tree in which every vertex has d + 1 neighbours, where d≥ 2. The contact process on such a tree is known to have three distinct phases. We consider the process on a finite subtree, namely the rooted tree of depth h and branching factor d, and relate the behaviour of the process on the infinite tree to its behaviour on the finite tree for large h. In the phase of strong survival, we show that with probability ɛ independent of h, the process on the subtree starting from a single infection survives for a time which is doubly exponential in h and almost exponential in the number of vertices of the finite tree. In the phase of weak survival on the infinite tree, the survival time on the finite tree is approximately linear in h. In the phase of no survival, the survival time on the finite tree is linear in h if one starts with all vertices initially infected, and bounded by a random variable (independent of h) with an exponential tail if one starts from a single infection. Received: 14 April 2000 / Revised version: 6 January 2001 / Published online: 9 October 2001     

A Structurally-Tunable 3-Hydroxyflavone Motif for Visible Light-Induced Carbon Monoxide-Releasing Molecules (CORMs)

Molecules that can be used to deliver a controlled amount of carbon monoxide (CO) have the potential to facilitate investigations into the roles of this gaseous molecule in biology and advance therapeutic treatments. This has led to the development of light-induced CO-releasing molecules (photoCORMs). A goal in this field of research is the development of molecules that exhibit a combination of controlled CO release, favorable biological properties (e.g., low toxicity and trackability in cells), and structural tunability to affect CO release. Herein, we report a new biologically-inspired organic photoCORM motif that exhibits several features that are desirable in a next-generation photoCORM. We show that 3-hydroxyflavone-based compounds are easily synthesized and modified to impart changes in absorption features and quantum yield for CO release, exhibit low toxicity, are trackable in cells, and can exhibit both O₂-dependent and -independent CO release reactivity.     

Formation of hyaluronic acid–ellagic acid microfiber hybrid hydrogels and their applications

Microfiber assemblies prepared from ellagic acid (EA) were functionalized with histidine (His) and dispersed in hyaluronic acid (HA) hydrogel microstructures. Swelling studies indicated that the hybrids had a relatively lower water uptake compared to HA and was pH dependent. The percentage swelling ratio for EA–His–HA hybrids was 48 % when 0.04 mg/mL of HA was incorporated and increased to 70 % when 1.2 mg/mL HA was integrated. Release studies using the dye crystal violet (CV) as a model drug showed that the rates were concentration-dependent. Further the hybrids were found to be thermally stable compared to HA. Cellular toxicity assays performed with normal rat kidney (NRK) cells indicated biocompatibility and adherence of the hybrids to the cells. Thus, we have developed a new family of hybrid hydrogels which readily formed on the EA–His functionalized microfibers and may have potential applications in drug delivery or tissue regeneration applications.     

Structure-directing roles and interactions of fluoride and organocations with siliceous zeolite frameworks

Interactions of fluoride anions and organocations with crystalline silicate frameworks are shown to depend subtly on the architectures of the organic species, which significantly influence the crystalline structures that result. One- and two-dimensional (2D) (1)H, (19)F, and (29)Si nuclear magnetic resonance (NMR) spectroscopy measurements establish distinct intermolecular interactions among F(-) anions, imidazolium structure-directing agents (SDA(+)), and crystalline silicate frameworks for as-synthesized siliceous zeolites ITW and MTT. Different types and positions of hydrophobic alkyl ligands on the imidazolium SDA(+) species under otherwise identical zeolite synthesis compositions and conditions lead to significantly different interactions between the F(-) and SDA(+) ions and the respective silicate frameworks. For as-synthesized zeolite ITW, F(-) anions are established to reside in the double-four-ring (D4R) cages and interact strongly and selectively with D4R silicate framework sites, as manifested by their strong (19)F-(29)Si dipolar couplings. By comparison, for as-synthesized zeolite MTT, F(-) anions reside within the 10-ring channels and interact relatively weakly with the silicate framework as ion pairs with the SDA(+) ions. Such differences manifest the importance of interactions between the imidazolium and F(-) ions, which account for their structure-directing influences on the topologies of the resulting silicate frameworks. Furthermore, 2D (29)Si{(29)Si} double-quantum NMR measurements establish (29)Si-O-(29)Si site connectivities within the as-synthesized zeolites ITW and MTT that, in conjunction with synchrotron X-ray diffraction analyses, establish insights on complicated order and disorder within their framework structures.     

Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines

Human alkyladenine DNA glycosylase (AAG) initiates the repair of a wide variety of (neutral or cationic) alkylated and deaminated purines by flipping damaged nucleotides out of the DNA helix and catalyzing the hydrolytic N-glycosidic bond cleavage. Unfortunately, the limited number of studies on the catalytic pathway has left many unanswered questions about the hydrolysis mechanism. Therefore, detailed ONIOM(M06-2X/6-31G(d):AMBER) reaction potential energy surface scans are used to gain the first atomistic perspective of the repair pathway used by AAG. The lowest barrier for neutral 1,N(6)-ethenoadenine (εA) and cationic N(3)-methyladenine (3MeA) excision corresponds to a concerted (A(N)D(N)) mechanism, where our calculated ΔG(?) = 87.3 kJ mol(-1) for εA cleavage is consistent with recent kinetic data. The use of a concerted mechanism supports previous speculations that AAG uses a nonspecific strategy to excise both neutral (εA) and cationic (3MeA) lesions. We find that AAG uses nonspecific active site DNA-protein π-π interactions to catalyze the removal of inherently more difficult to excise neutral lesions, and strongly bind to cationic lesions, which comes at the expense of raising the excision barrier for cationic substrates. Although proton transfer from the recently proposed general acid (protein-bound water) to neutral substrates does not occur, hydrogen-bond donation lowers the catalytic barrier, which clarifies the role of a general acid in the excision of neutral lesions. Finally, our work shows that the natural base adenine (A) is further inserted into the AAG active site than the damaged substrates, which results in the loss of a hydrogen bond with Y127 and misaligns the general base (E125) and water nucleophile to lead to poor nucleophile activation. Therefore, our work proposes how AAG discriminates against the natural purines in the chemical step and may also explain why some damaged pyrimidines are bound but are not excised by this enzyme.     

A Stable Silanol Triad in the Zeolite Catalyst SSZ‐70

Nests of three silanol groups are located on the internal pore surface of calcined zeolite SSZ‐70. 2D ¹H double/triple‐quantum single‐quantum correlation NMR experiments enable a rigorous identification of these silanol triad nests. They reveal a close proximity to the structure directing agent (SDA), that is, N,N′‐diisobutyl imidazolium cations, in the as‐synthesized material, in which the defects are negatively charged (silanol dyad plus one charged SiO^? siloxy group) for charge balance. It is inferred that ring strain prevents the condensation of silanol groups upon calcination and removal of the SDA to avoid energetically unfavorable three‐rings. In contrast, tetrad nests, created by boron extraction from B‐SSZ‐70 at various other locations, are not stable and silanol condensation occurs. Infrared spectroscopic investigations of adsorbed pyridine indicate an enhanced acidity of the silanol triads, suggesting important implications in catalysis.     

Defect Models of As‐Made High‐Silica Zeolites: Clusters of Hydrogen‐Bonds and Their Interaction with the Organic Structure‐Directing Agents Determined from 1H Double and Triple Quantum NMR Spectroscopy

Internal defect SiOH and SiO^? groups evolve during the structure formation of high‐Si zeolites in the presence of a cationic organic structure‐directing agent (SDA). These negatively charged defects do not completely disappear upon calcination. Herein we investigate the clustering of defect groups and their location within the pore walls of four zeolites. ZSM‐12, ZSM‐5, and SSZ‐74 have three clustered SiOH groups which are hydrogen‐bonded to SiO^?, whereas SSZ‐24 has only two. These defects interact with the structure‐directing quaternary ammonium ions preferably close to the charge center, unless steric shielding is present. The framework topologies of ZSM‐12, ZSM‐5, and SSZ‐24 have connected six‐rings where the organics interact with the defects. It is suggested that these six‐ring patterns form connectivity defects. SSZ‐74 is unique, it does not contain an extended six‐ring motif, so vacancy defects form instead.     

Computational and experimental evidence for the structural preference of phenolic C-8 purine adducts

The structural and spectral properties of (ortho and para) C8-aryl-purine adducts formed from carbon attachment by phenolic toxins were investigated through DFT calculations and UV-vis absorbance and emission studies. The global minima of both the deoxyadenosine (dA) and deoxyguanosine (dG) adducts adopted a syn conformation about the glycosidic bond due to the presence of an O5'-H...N3 hydrogen bond, where the anti minima are 20-30 kJ mol-1 higher in energy. While the nucleobase adducts are planar, the presence of the deoxyribose sugar induces a twist about the carbon-carbon bond connecting the phenol and nucleobase rings. ortho-Phenolic adducts are less twisted than the corresponding para adducts due to stabilization provided by an intramolecular O-H...N7 bond. Solvation calculations, in combination with UV-vis studies, demonstrate that the structural preference is solvent dependent, where solvents with hydrogen-bonding abilities disrupt the intramolecular O-H...N7 hydrogen bond such that a greater degree of twist is observed, and less polar solvents stabilize the planar structure. Indeed, the ratio of twisted to planar conformers is estimated to be as large as 50:50 in some aprotic solvents. Thus, the combined experimental and computational approach has provided a greater understanding of the structure of the ortho- and para-dA and dG C-bonded phenoxyl adducts as the first step to understanding the biological consequences of this form of DNA damage.