Aptamers are ssDNA or RNA that binds to wide variety of target molecules with high affinity and specificity produced by systematic evolution of ligands by exponential enrichment (SELEX). Compared to RNA aptamer, DNA aptamer is much more stable, favourable to be used in many applications. The most critical step in DNA SELEX experiment is the conversion of dsDNA to ssDNA. The purpose of this stud...

Targeting large transmembrane molecules, including receptor tyrosine kinases, is a major pharmacological challenge. Specific oligonucleotide ligands (aptamers) can be generated for a variety of targets through the iterative evolution of a random pool of sequences (SELEX). Nuclease-resistant aptamers that recognize the human receptor tyrosine kinase RET were obtained using RET-expressing cells a...

The RNA-binding protein Roquin is required to prevent autoimmunity. Roquin controls T-helper cell activation and differentiation by limiting the induced expression of costimulatory receptors such as tumor necrosis factor receptor superfamily 4 (Tnfrs4 or Ox40). A constitutive decay element (CDE) with a characteristic triloop hairpin was previously shown to be recognized by Roquin. Here we use S...

An evolution of antibiotic-resistant bacteria has resulted in the need for new antibiotics. β-Lactam based drugs are the most predominantly prescribed antibiotics to combat bacterial infections; however, production of β-lactamases, which catalyze the hydrolysis of the β-lactam bond of this class of antibiotics, by pathogenic bacteria such as Bacillus cereus, are rendering them useless. Some inh...

Currently, functional single-stranded oligonucleotide probes, termed aptamers, generated by an iterative technology, Systematic Evolution of Ligands by Exponential Enrichment (SELEX), are utilized to selectively target molecules or cells with high affinity. Aptamers hold considerable promise as multifunctional molecules or conjugates for challenging nanotechnologies or bioapplications now and i...

Transcription factors (TFs) play crucial roles in regulating gene expression through interactions with specific DNA sequences. Recently, the sequence motif of almost 400 human TFs have been identified using high-throughput SELEX sequencing. However, there remain a large number of TFs (∼800) with no high-throughput-derived binding motifs. Computational methods capable of associating known motifs...

Aptamers are nucleic acids referred to as chemical antibodies as they bind to their specific targets with high affinity and selectivity. They are selected via an iterative process known as 'selective evolution of ligands by exponential enrichment' (SELEX). Aptamers have been developed against numerous cancer targets and among them, many tumor cell-membrane protein biomarkers. The identification...

The observation of the D∗ sJ (2317), DsJ (2460), and SELEX D ∗ sJ (2632) states with properties differing considerably from what was expected has led to a renewed interest in hadron spectroscopy. In addition to these states, non-strange partners of the DsJ states have also been observed. Understanding the D∗ 0 and D ′ 1 states can provide important insights into the DsJ states. In this contribu...

We are investigating the rules that govern protein-DNA interactions, using a statistical mechanics based formalism that is related to the Boltzmann Machine of the neural net literature. Our approach is data-driven, in which probabilistic algorithms are used to model protein-DNA interactions, given SELEX and/or phage data as input. In the current report, we trained the network using SELEX data, ...