To appear in RNA (rnajournal.org). Abstract It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low complexity structures. Early experimental results suggest that having a structurally diverse library which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to gen...

It is suggested that the narrow meson state seen in the the SELEX experiment is a (cs̄ss̄) tetraquark state. Characteristics of other possible tetraquarks formed out of c and s quarks and antiquarks are considered. SELEX experiment has reported [1] a puzzling narrow meson state at a mass of 2632.6± 1.6 MeV/c which decays preferentially to D s (cs̄) + η(548) rather than to D(cd̄)+K or D(cū)+K. In th...

We observe a signal for the doubly charmed baryon Ξcc in the decay mode Ξ + cc → pDK to complement the previous reported decay Ξcc → Λc Kπ in data from SELEX, the charm hadro-production experiment at Fermilab. In this new decay mode we observe an excess of 5.62 events over a combinatoric background estimated by event mixing to be 1.38 ± 0.13 events. The mixed background has Gaussian statistics,...

It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structu...

The generation of single-stranded DNA (ssDNA) molecules plays a key role in the SELEX (Systematic Evolution of Ligands by EXponential enrichment) combinatorial chemistry process and numerous molecular biology techniques and applications, such as DNA sequencing, single-nucleotide polymorphism (SNP) analysis, DNA chips, DNA single-strand conformation polymorphism (SSCP) analysis and many other te...

The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However,...

Age-related macular degeneration (AMD) is the main cause of loss of sight in the world and is characterized by neovascularization of the macula. The factors producing choroidal vascularization involve various growth factors, including the vascular endothelial growth factor (VEGF(165)). In this context, the systematic evolution of ligands by exponential enrichment (SELEX) became a tool for devel...

SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] ...

An initial step in amyloid-β (Aβ) production includes amyloid precursor protein (APP) cleavage via β-Site amyloid precursor protein cleaving enzyme 1 (BACE1). Increased levels of brain Aβ have been implicated in the pathogenesis of Alzheimer's disease (AD). Thus, β-secretase represents a primary target for inhibitor drug development in AD. In this study, aptamers were obtained from combinatoria...

We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the processes of affinity selection and amplification of target-binding oligonucleotides, and an electrophoretic DNA manipulation scheme for the coupling of these processes, which are required to occ...