Search results for "aptamers"

Stability of a Split Streptomycin Binding Aptamer

2016

Here we investigated the stability of an aptamer, which is formed by two RNA strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystal structure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycin binding with a free energy of ΔGbind° = −101.7 kJ mol–1. Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (koff-COMPLEX = 0.22 ± 0.16 s–1) for the …

Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing

2018

AbstractAptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live…

Measuring single small molecule binding via rupture forces of a split aptamer.

2011

The rupture force of a split (bipartite) aptamer that forms binding pockets for adenosine monophosphate (AMP) was measured by atomic force spectroscopy. Changes in the rupture force were observed in the presence of AMP, while this effect was absent when mutant aptamers or inosine were used. Thus, changes in the rupture force were a direct consequence of specific binding of AMP to the split aptamer. The split aptamer concept allowed the detection of nonlabeled AMP and enabled us to determine the dissociation constant on a single-molecule level.

Functional Fibronectin Adsorption on Aptamer-Doped Chitosan Modulates Cell Morphology by Integrin-Mediated Pathway.

2019

A decisive step in cell-biomaterial interaction is represented by the adsorption of proteins at the interface, whose fine control may be useful to trigger proper cell response. To this purpose, we can selectively control protein adsorption on biomaterials by means of aptamers. Aptamers selected to recognize fibronectin dramatically enhance chitosan ability to promote cell proliferation and adhesion, but the underlying biological mechanism remains unknown. We supposed that aptamers contributed to ameliorate the adsorption of fibronectin in an advantageous geometrical conformation for cells, thus regulating their morphology by the proper activation of the integrin-mediated pathway. We investi…

The selection of aptamers specific for membrane molecular targets

2010

AbstractA growing number of RNA aptamers have been selected experimentally using the SELEX combinatorial approach, and these aptamers have several advantages over monoclonal protein antibodies or peptides with respect to their applications in medicine and nanobiotechnology. Relatively few successful selections have been reported for membrane molecular targets, in contrast to the situation with non-membrane molecular targets. This review compares the procedures and techniques used in selections against membrane proteins and membrane lipids. In the case of membrane proteins, the selections were performed against soluble protein fragments, detergent-membrane protein mixed micelles, whole cells…

Targeting cancer with peptide aptamers

2011

Renaud Seigneuric 1,2 , Jessica Gobbo 1,2 , Pierre Colas 3 , Carmen Garrido 1,2 1 Heat Shock Proteins and Cancer, INSERM, UMR 866 IFR 100, Faculty of Medicine, 7 Boulevard Jeanne D'Arc, 21000 Dijon, France 2 Universite de Bourgogne, Dijon, France 3 CNRS USR 3151, P2I2 Group, Station Biologique, Roscoff, Bretagne, France Received: June 22, 2011; Accepted: June 24, 2011; Published: June 24, 2011; Correspondence: Renaud Seigneuric, email: // // Abstract A major endeavour in cancer chemotherapy is to develop agents that specifically target a biomolecule of interest. There are two main classes of targeting agents: small molecules and biologics. Among biologics (e.g.: antibodies), DNA, RNA but al…

A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme.

2017

International audience; The quadruplex-based DNAzyme system is one of the most useful artificial enzymes or catalysts; their unique properties make them reliable alternatives to proteins for performing catalytic transformation. The first prototype of a thermally stable DNAzyme system is presented. This thermophilic DNAzyme is capable of oxidizing substrates at high temperatures (up to 95 degrees C) and long reaction times (up to 18 h at 75 degrees C). The catalytic activity of the DNAzymes were investigated with the standard peroxidase-mimicking oxidation of 2,2'-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid) (ABTS) by H2O2. The step-by-step design of this unique heat-activated G-quadrup…

Novel Lipid and Polymeric Materials as Delivery Systems for Nucleic Acid Based Drugs

2015

Nucleic acid based drugs (NADBs) are short DNA/RNA molecules that include among others, antisense oligonucleotides, aptamers, small interfering RNAs and micro-interfering RNAs. Despite the different mechanisms of actions, NABDs have the ability to combat the effects of pathological gene expression in many experimental systems. Thus, nowadays, NABDs are considered to have a great therapeutic potential, possibly superior to that of available drugs. Unfortunately, however, the lack of effective delivery systems limits the practical use of NABDs. Due to their hydrophilic nature, NABDs cannot efficiently cross cellular membrane; in addition, they are subjected to fast degradation by cellular and…

DNA Nanostructures in Cell Biology and Medicine

2017

An aptamer-gated silica mesoporous material for thrombin detection.

2013

An aptamer-capped mesoporous material for the selective and sensitive detection of &-thrombin in human plasma and serum has been prepared and characterised.