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Biomedical subjects

Emin Oroudjev

Publications and source records attributed to Emin Oroudjev.

8 recordsLinked to original sources
PubMed2005

Origin of the long-range attraction between surfactant-coated surfaces.

We compare the "long-range hydrophobic forces" measured (i) in the "symmetric" system between two mica surfaces that had been rendered hydrophobic by the adsorption of a double-chained cationic surfactant, and (ii) between one such hydrophobic surface and a hydrophilic surface of bare mica ("asymmetric" case). In both cases, the forces were purely attractive, stronger than van der Waals, and of long-range, as previously reported, with those of the asymmetric, hydrophobic-hydrophilic system being even stronger and of longer range. Atomic force microscopy images of these surfaces show that the monolayers transform into patchy bilayers when the surfaces are immersed in water, and that the resulting surfaces contain large micrometer-sized regions of positive charges (bilayer) and negative charges (bare mica) while remaining overall neutral. The natural alignment of oppositely charged domains as two such surfaces approach would result in a long-range electrostatic attraction in water, but the short-range, "truly hydrophobic" interaction is not explained by these results.

Aluminum Silicates↗
PubMed2004

Building programmable jigsaw puzzles with RNA.

One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules.

Algorithms↗
PubMed2004

Atomic force microscopy imaging and pulling of nucleic acids.

Recent advances in atomic force microscopy (AFM) imaging of nucleic acids include the visualization of DNA and RNA incorporated into devices and patterns, and into structures based on their sequences or sequence recognition. AFM imaging of nuclear structures has contributed to advances in telomere research and to our understanding of nucleosome formation. Highlights of force spectroscopy or pulling of nucleic acids include the use of DNA as a programmable force sensor, and the analysis of RNA flexibility and drug binding to DNA.

DNA↗
PubMed2003

Molecular nanosprings in spider capture-silk threads.

Spider capture silk is a natural material that outperforms almost any synthetic material in its combination of strength and elasticity. The structure of this remarkable material is still largely unknown, because spider-silk proteins have not been crystallized. Capture silk is the sticky spiral in the webs of orb-weaving spiders. Here we are investigating specifically the capture spiral threads from Araneus, an ecribellate orb-weaving spider. The major protein of these threads is flagelliform protein, a variety of silk fibroin. We present models for molecular and supramolecular structures of flagelliform protein, derived from amino acid sequences, force spectroscopy (molecular pulling) and stretching of bulk capture web. Pulling on molecules in capture-silk fibres from Araneus has revealed rupture peaks due to sacrificial bonds, characteristic of other self-healing biomaterials. The overall force changes are exponential for both capture-silk molecules and intact strands of capture silk.

Animals↗
PubMed2002

Artificial human telomeres from DNA nanocircle templates.

Human telomerase is a reverse-transcriptase enzyme that synthesizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification protocol assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor. We show that artificial telomeres can be engineered on human chromosomes by this approach. This strategy allows for the preparation of synthetic telomeres for biological and structural study of telomeres and proteins that interact with them, and it raises the possibility of telomere engineering in cells without expression of telomerase itself. Finally, the results provide direct physical support for a recently proposed rolling-circle mechanism for telomerase-independent telomere elongation.

Animals↗