Vault ribonucleoprotein particles and the central mass of the nuclear pore complex

Nuclear pore complexes (NPCs) are macromolecular pores that span the nuclear envelope and undergo conformational changes in response to changes in cisternal calcium levels. Depletion of cisternal calcium leads to the appearance of a mass within the pore. The identity and role of this central mass remain unknown, although some studies suggest they are vault complexes. Vault complexes are 13 MDa ribonucleoproteins found in the cytoplasm and recently in the nuclei of some species, suggesting that they associate with NPCs to cross the nuclear envelope. Using Förster resonance energy transfer (FRET) measurements between labeled vaults and NPCs, we find significant energy transfer suggesting that vaults and NPCs are closely associated at the nuclear envelope. This is supported by high‐resolution electron microscopy measurements revealing significant spatial correlations between gold‐labeled vaults and NPCs. As the location of the central mass in the NPC is dependent on cisternal calcium levels, FRET signals under conditions of varying cisternal calcium were also measured and shown to undergo significant changes. Together, these findings suggest that the central mass observed in NPCs may be, at least in part, due to the presence of vaults in the pore. Possible roles in cyto‐nuclear trafficking are discussed.     

Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling,synthesis and biological testing

Journal of Computer-Aided Molecular Design - The problem of designing new antiviral drugs against Human Cytomegalovirus (HCMV) was addressed using the Online Chemical Modeling Environment (OCHEM)....     

Versatile site-specific conjugation of small molecules to siRNA using click chemistry

We have previously demonstrated that conjugation of small molecule ligands to small interfering RNAs (siRNAs) and anti-microRNAs results in functional siRNAs and antagomirs in vivo. Here we report on the development of an efficient chemical strategy to make oligoribonucleotide-ligand conjugates using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) or click reaction. Three click reaction approaches were evaluated for their feasibility and suitability for high-throughput synthesis: the CuAAC reaction at the monomer level prior to oligonucleotide synthesis, the solution-phase postsynthetic "click conjugation", and the "click conjugation" on an immobilized and completely protected alkyne-oligonucleotide scaffold. Nucleosides bearing 5'-alkyne moieties were used for conjugation to the 5'-end of the oligonucleotide. Previously described 2'- and 3'-O-propargylated nucleosides were prepared to introduce the alkyne moiety to the 3' and 5' termini and to the internal positions of the scaffold. Azido-functionalized ligands bearing lipophilic long chain alkyls, cholesterol, oligoamine, and carbohydrate were utilized to study the effect of physicochemical characteristics of the incoming azide on click conjugation to the alkyne-oligonucleotide scaffold in solution and on immobilized solid support. We found that microwave-assisted click conjugation of azido-functionalized ligands to a fully protected solid-support bound alkyne-oligonucleotide prior to deprotection was the most efficient "click conjugation" strategy for site-specific, high-throughput oligonucleotide conjugate synthesis tested. The siRNA conjugates synthesized using this approach effectively silenced expression of a luciferase gene in a stably transformed HeLa cell line.     

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 Linear Oligomers of (R)-3-Hydroxybutyrate and Solid-State Structural Investigations by electron microscopy and X-ray scattering

Repetitive treatment of the biopolymer P(3-HB) (molecular weight > 10⁵ Dalton, storage or s-P(3-HB)), with lithium hexamethyl disilazanid (LHMDS) at ?70° in THF leads to a mixture of oligomers with increasingly sharp distribution around a 15-, 30-, and 45mer. Discrete fragments are also isolated when P(3-HB) is heated under reflux (89°) in neat Et₃N. Linear oligo(3-HB) derivatives ( 3-7 ) containing up to 96 3-HB units are synthesized using an exponential segment-coupling strategy. These oligomers are used to calibrate size-exclusion chromatography columns for the analysis of oligo(3-HB) samples from the different sources. The linear oligo-(3-HB) derivatives also served as a model with respect to the physical properties of high molecular weight P(3-HB) and were investigated as such by transmission electron microscopy (TEM) and by small- and wide-angle X-ray scattering (SAXS and WAXS). The thicknesses of the lamellar crystallites (long periods) formed by the 8mer, 16mer, and 32mer, are ca. 26, 52, and 53 Å, respectively, indicating that the 32mer molecules are folded once, very tightly, into a ‘hair-pin’-type conformation. High-molecular-weight P(3-HB), which was crystallized in a similar way, also has a lamellar crystallite thickness of ca. 50–65 Å. Thus, the treatment of P(3-HB) with LHMDS at low temperature causes etching of the amorphous regions, an effect well known in polymer science for studying the regularity of chain folding. The ca. 50-Å packing within the tight folds of P(3-HB) is discussed in view of its possible function in ion transport through cell membranes.     

13C NMR investigation of tautomeric and acid-base equilibria of pyrazolone T and three analogs

Pyrazolone T and three derivatives have been characterized by ¹³C and, in part, ¹⁵N nmr at several pH values. The ¹³C chemical shifts have been assigned at, or near, the equivalence points and pK_a values of these four compounds. Closely situatued quaternary carbon signals were assigned by means of a heteronuclear chemical shift correlation (FLOCK) experiment which is sensitive to, and was optimized for, 3-bond C-H couplings. The ¹³C chemical shift data indicate the existence of both tautomeric and acid-base equilibria and demonstrate that the four congeners exist in surprisingly different forms at certain common pH values.     

On functions that are trivial cocycles for a set of irrationals. II

Two results are obtained about the topological size of the set of irrationals for which a given function is a trivial cocycle. An example of a continuous function which is a coboundary with non- cobounding function is constructed.