Besides canonical double-strand DNA promoters, multisubunit RNAPs (RNA polymerases) recognize a number of specific single-strand DNA and RNA templates, resulting in synthesis of various types of RNA transcripts. The general recognition principles and the mechanisms of transcription initiation on these templates are not fully understood. To investigate further the molecular mechanisms underlying...

A blue fluorescent RNA was applied to modular blue fluorescent RNA sensors, wherein a "recognition" event of the target molecule by the aptamer domain is transmitted through a "communication" module, to a "signaling" fluorescent RNA domain, which "lights up".

Positive-strand RNA viruses direct different virus-specific processes during their infection of host cells. Fundamental events such as viral RNA genome replication are controlled by viral regulatory RNA elements (REs). Here, we have investigated the possibility of specifically modulating the action of a viral RE using RNA aptamer technology. Through rational design, a tombusvirus RE, which has ...

A major goal of synthetic biology is to control cell behavior. RNA-mediated genetic switches (RNA switches) are devices that serve this purpose, as they can control gene expressions in response to input signals. In general, RNA switches consist of two domains: an aptamer domain, which binds to an input molecule, and an actuator domain, which controls the gene expression. An input binding to the...

Live cell imaging of RNA or their protein binding partners is crucial to obtain an authentic picture of RNA transcription, processing and trafficking. The development of methods for tracking of specific target RNAs in diverse cellular systems has been approached by different strategies including synthetic dyes, molecular beacons and genetically encoded RNA labels. In this work, we challenged cu...

Riboswitches, whose folding is controlled by binding of metabolites to the aptamer domain, regulate downstream gene expression. Folding properties of the aptamer strongly influence the conformation of the downstream expression platform, which controls transcription termination or translation initiation. We have characterized the energy landscape of the add riboswitch aptamer quantitatively by u...

Aptamers have emerged as a new class of small molecule ligands. These short, single-stranded oligonucleotides can be produced through simple chemical synthesis, making them easier and less costly to produce than antibodies. We synthesized an RNA aptamer probe specific for human CD4 using a reported sequence and investigated the potential use of this probe in cell phenotyping. Studies in culture...

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...

Hepatitis C virus (HCV) replication is dependent on the existence of several highly conserved functional genomic RNA domains. The cis-acting replication element (CRE), located within the 3' end of the NS5B coding region of the HCV genome, has been shown essential for efficient viral replication. Its sequence and structural features determine its involvement in functional interactions with viral...

GTP plays a central role in diverse cellular processes, and at least three percent of the proteins in the human proteome bind GTP. The fundamental role played by GTP in cells, as well as the emerging realization that the functions of biological proteins and RNAs may not be as distinct as once thought, led us to hypothesize that RNA molecules that bind GTP might also be widespread in nature. To ...