aptamers, or single stranded oligonucleotides, are produced by systematic evolution of ligands by exponential enrichment, abbreviated as selex. in the amplification and regeneration step of selex technique, dsdna is conversed to ssdna. asymmetric pcr is one of the methods used for the generation of ssdna. the purpose of this study was to design a random dna library for selection of aptamers wit...

Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all the...

Using the systematic evolution of ligands by exponential enrichment (SELEX) method, we identified oligonucleotides that bind to the first extracellular domain of the Orai1 protein with high affinities and high specificities. These ligands were isolated from a random single-strand DNA (ssDNA) library with 40 randomized sequence positions, using synthesized peptides with amino acid sequences iden...

The generation of single-stranded DNA (ssDNA) from double-stranded PCR products is an essential step in the selection of aptamers by systematic evolution of ligands by exponential enrichment (SELEX). Magnetic separation with streptavidin-coated beads is always the most commonly used method. Recently, two size separation methods derived from unequal primers with chemical or structural modificati...

In this paper, we report on a case study conducted with the MASTRO-I system at SELEX Sistemi Integrati, a world’s leading company in the provision of integrated defence and air traffic systems. MASTRO-I is a tool for ontology-based data integration that combines advanced services for reasoning over ontologies with the capabilities provided by relational data federation tools, used for wrapping ...

Plasmodium falciparum malaria parasites invade and remodel human red blood cells (RBCs) by trafficking parasite-synthesized proteins to the RBC surface. While these proteins mediate interactions with host cells that contribute to disease pathogenesis, the infected RBC surface proteome remains poorly characterized. Here we use a novel strategy (I-SELEX) to discover high affinity aptamers that se...

BACKGROUND Synthesizing and characterizing aptamers with high affinity and specificity have been extensively carried out for analytical and biomedical applications. Few publications can be found that describe structure-activity relationships (SARs) of candidate aptamer sequences. METHODOLOGY This paper reports pattern recognition with support vector machine (SVM) classification techniques for...

Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic ...

Nasopharyngeal carcinoma (NPC) is one of the most prevailing cancers in southern China and southern Asia. Because of the nonspecific symptoms and lack of effective biomarker, most patients are diagnosed at advanced stages, resulting in poor 5-year survival rate. To identify a novel NPC biomarker facilitating early detection and effective therapy of NPC, a two-step strategy consisting of cancer ...

We have used systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers against aminoglycoside antibiotics. The SELEX rounds were toggled against four pairs of aminoglycosides with the goal of isolating reagents that recognize conserved structural features. The resulting aptamers bind both of their selection targets with nanomolar affinities. They also bind the le...