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Molecular Recognition Properties (molecular + recognition_property)
Selected AbstractsEngineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite greenJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2009Xing Zhang Abstract In previous work, Vibrio proteolyticus 5S rRNA was shown to stabilize 13,50 nucleotide "guest" RNA sequences for expression in Escherichia coli. The expressed chimeric RNAs accumulated to high levels in E. coli without being incorporated into ribosomes and without obvious effects on the host cells. In this work, we inserted sequences encoding known aptamers recognizing a protein and an organic dye into the 5S rRNA carrier and showed that aptamer function is preserved in the chimeras. A surface plasmon resonance competitive binding assay demonstrated that a vascular endothelial growth factor (VEGF) aptamer/5S rRNA chimera produced in vitro by transcriptional runoff could compete with a DNA aptamer for VEGF, implying binding of the growth factor by the VEGF "ribosomal RNA aptamer." Separately, a 5S rRNA chimera displaying an aptamer known to increase the fluorescence of malachite green (MG) also enhanced MG fluorescence. Closely related control rRNA molecules showed neither activity. The MG aptamer/5S rRNA chimera, like the original MG aptamer, also increased the fluorescence of other triphenyl methane (TPM) dyes such as crystal violet, methyl violet, and brilliant green, although less effectively than with MG. These results indicate that the molecular recognition properties of aptamers are not lost when they are expressed in the context of a stable 5S rRNA carrier. Inclusion of the aptamer in a carrier may facilitate production of large quantities of RNA aptamers, and may open an approach to screening aptamer libraries in vivo. Copyright © 2009 John Wiley & Sons, Ltd. [source] Single-molecule pair studies of the interactions of the ,-GalNAc (Tn-antigen) form of porcine submaxillary mucin with soybean agglutininBIOPOLYMERS, Issue 9 2009Marit Sletmoen Abstract Mucins form a group of heavily O -glycosylated biologically important glycoproteins that are involved in a variety of biological functions, including modulating immune response, inflammation, and adhesion. Mucins are also involved in cancer and metastasis and often express diagnostic cancer antigens. Recently, a modified porcine submaxillary mucin (Tn-PSM) containing GalNAc,1- O -Ser/Thr residues was shown to bind to soybean agglutinin (SBA) with ,106 -fold enhanced affinity relative to GalNAc,1- O -Ser, the pancarcinoma carbohydrate antigen. In this study, dynamic force spectroscopy is used to investigate molecular pairs of SBA and Tn-PSM. A number of force jumps that demonstrate unbinding or rebinding events were observed up to a distance equal to 2.0 ,m, consistent with the length of the mucin chain. The unbinding force increased from 103 to 402 pN with increasing force loading rate. The position of the activation barrier in the energy landscape of the interaction was 0.1 nm. The lifetime of the SBA,TnPSM complex in the absence of applied force was determined to be in the range 1.3,1.9 s. Kinetic parameters describing the rate of dissociation of other sugar lectin interactions are in the range 3.3 × 10,3,2.5 × 10,3 s. The long lifetime of the SBA-TnPSM complex is compatible with a binding model in which lectin molecules "bind and jump" from ,-GalNAc residue to ,-GalNAc residue along the polypeptide chain of Tn-PSM before dissociating. These findings have important implications for the molecular recognition properties of mucins. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 719,728, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Reactive Sieving with Foldamers: Inspiration from Nature and Directions for the FutureCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2008Ronald Abstract Over the past several decades, chemists have designed a myriad of supramolecular scaffolds for the purpose of mimicking enzyme behavior and creating more advanced catalysts. Foldamers, one class of supramolecular structures that feature rapid, modular synthesis and dynamic structural properties and have been widely investigated for their molecular recognition properties. Specifically, our group has designed a reactive m -phenyleneethynylene foldamer, which mimics the selective properties ("reactive sieving") of the isoleucine tRNA synthetase enzyme. In this concept we discuss examples that have inspired our research as well as potential directions for future advancement of this field. [source] N -Linked Glycosylated , -Peptides Are Resistant to Degradation by Glycoamidase ACHEMISTRY & BIODIVERSITY, Issue 12 2005Matthew , -Peptides are resistant to degradation by a variety of proteolytic enzymes that rapidly degrade natural , -peptides. This is one of many characteristics that make , -peptides an attractive class of compounds for drug discovery efforts. To further understand the molecular recognition properties of , -peptides and the ability of enzymes to degrade them, we have synthesized a series of N- linked glycosylated , - and , -peptides, and tested their stability towards a glycosidase. We found that glyco- , -peptides that contain N- acetylglucosamine (1) or N,N -diacetylchitobiose (2) are completely stable to degradation by glycoamidase A. In comparison, the glyco- , -peptides 3 and 4 containing N -acetylglucosamine or N,N -diacetylchitobiose are degraded. Inhibition experiments using increasing concentrations of a glyco- , -peptide fail to inhibit degradation of the corresponding glyco- , -peptide, even when the glyco- , -peptide is at a 128-fold higher concentration than the glyco- , -peptide. Evidently, the glyco- , -peptides have a much weaker affinity for the active site of the glycosidase than the corresponding glyco- , -peptide. These and the results with proteolytic enzymes suggest that the additional CH2 group introduced into the , -amino acid residues causes , -peptides not to be recognized by hydrolytic enzymes. The results described herein suggest the potential of , -peptides that are functionalized with carbohydrates for biological and biomedical investigations, without having to be concerned about the carbohydrate being removed. [source] | ||||||||||