An RNA aptamer that interferes with the DNA binding of the HSF transcription activator

Heat shock factor (HSF) is a conserved and highly potent transcription activator. It is involved in a wide variety of important biological processes including the stress response and specific steps in normal development. Reagents that interfere with HSF function would be useful for both basic studies and practical applications. We selected an RNA aptamer that binds to HSF with high specificity. Deletion analysis defined the minimal binding motif of this aptamer to be two stems and one stem–loop joined by a three-way junction. This RNA aptamer interferes with normal interaction of HSF with its DNA element, which is a key regulatory step for HSF function. The DNA-binding domain plus a flanking linker region on the HSF (DL) is essential for the RNA binding. Additionally, this aptamer inhibits HSF-induced transcription in vitro in the complex milieu of a whole cell extract. In contrast to the previously characterized NF-κB aptamer, the HSF aptamer does not simply mimic DNA binding, but rather binds to HSF in a manner distinct from DNA binding to HSF

TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages

Transcription in eukaryotes is a multistep process involving the assembly and disassembly of numerous inter- and intramolecular interactions between transcription factors and nucleic acids. The roles of each of these interactions and the regions responsible for them have been identified and studied primarily by the use of mutants, which destroy the inherent properties of the interacting surface. A less intrusive but potentially effective way to study the interactions as well as the surfaces responsible for them is the use of RNA aptamers that bind to the interacting factors. Here, we report the isolation and characterization of high-affinity RNA aptamers that bind to the yeast general transcription factor TFIIB. These aptamers fall into two classes that interfere with TFIIB's interactions with either TBP or RNA polymerase II, both of which are crucial for transcription in yeast. We demonstrate the high affinity and specificity of these reagents, their effect on transcription and preinitiation complex formation and discuss their potential use to address mechanistic questions in vitro as well as in vivo

Antibacterial nanoparticles based on fluorescent 3-substituted uridine analogue

With a sudden and rapid increase in the spread of antimicrobial resistance, there is an urgent need for the development of novel antimicrobial therapies. Nanoparticles with antimicrobial activity provide advantages such as improved solubility, permeability, stability and selectivity. In this study, a uridine-scaffold was connected to a pyrene fluorescent unit to obtain novel compound UPy via an economical and straightforward route. Further, fluorescent organic nanoparticles (FONs) were prepared via self assembly of UPy and were found to have antibacterial activity towards Gram positive bacteria. The fluorescent nature of the FONs allowed us to identify a binding partner and propose mechanism of action in vivo. We believe that UPy can be an excellent starting point for the development of novel, potent and selective antimicrobial nanotherapeutics