Cy5-Labeled Phosphatidylcholine

Russian Journal of Bioorganic Chemistry - Fluorescent lipid probes are widely used as tools for studying the properties of biological membranes and for studies of such biological functions of...     

Lipophilic prodrugs of a triazole-containing colchicine analogue in liposomes: Biological effects on human tumor cells

Colchicine site binders—blockers of tubulin polymerization—are potential antimitotic agents for anticancer therapy. To reduce their systemic toxicity and improve biodistribution, encapsulation in nanosized liposomes may be employed. Liposomes present a convenient means for preparation of injectable for-mulations of hydrophobic compounds, however colchicine as such is known to leak through the lipid bilayer. In this study, newly synthesized triazole-containing analogues of colchicine and allocolchicine, and their palmitic and oleic esters (lipophilic prodrugs) were tested for anti-proliferative activity and apoptosis-inducing potential. In contrast to colchicine conjugates, whose activities ranged with those of colchicine, allocolchicine derivatives exhibited drastically lower effects and were discarded. Liposomes of about 100 nm in diameter composed of egg phosphatidylcholine-yeast phosphatidylinositol-palmitic or oleic prodrug, 8: 1: 1, by mol, were prepared by standard extrusion technique and tested in a panel of four human tumor cell lines. Liposome formulations preserved the biological activities of the parent colchicinoid the most towards human epithelial tumor cells. Moreover, liposomal form of the oleoyl bearing colchicinoid inhibited cell proliferation more efficiently than free lipophilic prodrug. Due to substantial loading capacity of the liposomes, the dispersions contain sufficient concentration of the active agent to test wide dose range in experiments on systemic administration to animals.     

Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets

Identification of single nucleotide polymorphisms (SNPs) is a key element in sequence-based genetic analysis. Next generation sequencing offers a cost-effective basis to generate the necessary, large sequence data sets, and bioinformatic methods are being developed to process sequencing machine readouts. We were interested in detection of SNPs in a 350 kb region of an EMS-mutagenized Arabidopsis chromosome 3. The region was selectively analyzed using PCR-generated, overlapping fragments for Solexa sequencing. The ensuing reads provided a high coverage and were processed bioinformatically. In order to assess the SNP candidates obtained with a frequently used alignment program and SNP caller, we developed an additional method that allows the identification of high confidence SNP loci. The method can easily be applied to complete genome sequence data of sufficient coverage.     

The Study of Possible A and B Conformations of Alternating DNA Using a New Program for Conformational Analysis of Duplexes (CONAN)

Abstract

A new program, CONAN has been designed for CONformational ANalysis of oligonucleotide duplexes with natural and modified bases. It allows to model both regular DNA fragments with different types of symmetry and irregular ones including bends, junctions, mismatched pairs and base lesions. Computations and minimization of the energy are performed in a space of internal structural variables chosen to build start structure easier and conveniently analyze the results obtained. These internal structural variables determine mutual base-base and base-sugar arrangement and sugar puckering. The analytical closure procedure is applied both to sugar rings and to backbone fragments between adjacent sugars. For more effective energy minimization, analytical gradient is calculated. The CONAN was applied to the search for low-energy conformations of poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) duplexes. Extended regions of low-energy A and B conformations are revealed and characterized. These regions contain structures with different relative values of helical twist, τ, for pur-pyr and pyr-pur steps, namely, conformations with τ(pur-pyr)>τ(pyr-pur) and with τ(pur-pyr)<τ(pyr-pur). Two types of sugar puckering were found for B-form low-energy conformations, the first type with all C2′-endo sugar residues and the second one—;with C2′-endo purines and O1′-endo pyrimidines. The calculated conformations are compared with X-ray diffraction data for crystals and fibers and NMR data for solution.     

Expression patterns of the ADAMs in early developing chicken cochlea

Members of the ADAM (a disintegrin and metalloprotease) family are type I transmembrane proteins involved in biological processes of proteolysis, cell adhesion, cell–matrix interaction, as well as in the intracellular signaling transduction. In the present study, expression patterns of seven members of the ADAM family were investigated at the early stages of the developing cochlea by in situ hybridization. The results show that each individual ADAM is expressed and regulated in the early developing cochlea. ADAM9, ADAM10, ADAM17, and ADAM23 are initially and widely expressed in the otic vesicle at embryonic day 2.5 (E2.5) and in the differential elements of the cochlear duct at E9, while ADAM12 is expressed in acoustic ganglion cells at E7. ADAM22 is detectable in cochlear ganglion cells as early as from E4 and in the basilar papilla from E7. Therefore, the present study extends our previous results and suggests that ADAMs also play a role in the early cochlear development.