Transfer DNA (T-DNA) insertion mutants are often used in forward and reverse genetics to reveal the molecular mechanisms of a particular biological process in plants. To generate T-DNA insertion mutants, T-DNA must be inserted randomly in the genome through transformation mediated by Ag ...

EMS mutant analysis is a routine experiment to identify new players in a specific biological process or signaling pathway using forward genetics. It begins with the generation of mutants by treating Arabidopsis seeds with EMS. A mutant with a phenotype of interest (mpi) is obtained by screeni ...

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miR ...

Zinc finger nucleases (ZFNs) are proteins engineered to make site-specific double-strand breaks (DSBs) in a DNA sequence of interest. Imprecise repair of the ZFN-induced DSBs by the nonhomologous end-joining (NHEJ) pathway results in a spectrum of mutations, such as nucleotide substi ...

Bioinformatic tools are an increasingly important resource for Arabidopsis researchers. With them, it is possible to rapidly query the large data sets covering genomes, transcriptomes, proteomes, epigenomes, and other “omes” that have been generated in the past decade. Often these to ...

The volume of Arabidopsis information has increased enormously in recent years as a result of the sequencing of the reference genome and other large-scale functional genomics projects. Much of the data is stored in public databases, where data are organized, analyzed, and made freely acces ...

An understanding of basic methods in Arabidopsis tissue culture is beneficial for any laboratory working on this model plant. Tissue culture refers to the aseptic growth of cells, organs, or plants in a controlled environment, in which physical, nutrient, and hormonal conditions can all be ea ...

The Arabidopsis-related model species (ARMS) Thellungiella salsuginea and Thellungiella parvula have generated broad interest in salt stress research. While general growth characteristics of these species are similar to Arabidopsis, some aspects of their life cycle require ...

Growing healthy plants is essential for the advancement of Arabidopsis thaliana (Arabidopsis) research. Over the last 20 years, the Arabidopsis Biological Resource Center (ABRC) has collected and developed a series of best-practice protocols, some of which are presented in this chap ...

A caged fluorescent nucleic acid probe, which contains a nucleotide modified with one photolabile nitrobenzyl unit and two hybridization-sensitive thiazole orange units, has been synthesized for area-specific fluorescence imaging of RNA in a cell. The probe emits very weak fluore ...

Significant efforts have been devoted to the development of techniques allowing the investigation of viral mRNA progression during the replication cycle. We herein describe the use of sequence-specific FIT–PNA (Forced Intercalation Peptide Nucleic Acids) probes which contain a ...

Molecular beacons are oligonucleotide (DNA or RNA) probes that have become increasingly important tools for RNA sensitive detection both in vitro and in living cells. From their inception, molecular beacons have been used to determine the expression levels of RNA transcripts, but they al ...

There is a lack of methods for high-throughput functional microRNA (miRNA) profiling. In this chapter, we describe a recombinant adeno-associated virus-based miRNA sensor array (miRNA Asensor array), which is able to profile functional miRNAs in cultured cells. The preparation of an mi ...

MicroRNAs play an important role in gene regulation and disease etiology and are blood-based biomarkers of diseases. Here, we describe a protein-facilitated affinity capillary electrophoresis (ProFACE) method for ultra-sensitive direct miRNA detection as low as 300,000 molec ...

Fluorescent in situ hybridization (FISH) is a powerful technology for studying the chromosome organization and aberrations as well as for searching the homology between chromosomal regions in mammals. Currently, FISH is used as a simple, rapid, and reliable technique for analyzing ch ...

Peptide nucleic acid (PNA) openers have the unique ability to invade double-stranded DNA with high efficiency and sequence specificity, making it possible to detect short (about 20 bp), single-copy bacterial DNA sequences. PNA openers bind to a target signature site on one strand of bacteri ...

Graphene oxide is chemically functionalized using planar structured first generation polyamidoamine dendrimer (G1PAMAM) to form graphene core GG1PAMAM. The monolayer of GG1PAMAM is anchored on the 3-mercapto propionic acid monolayer pre-immobilized onto a gold transduce ...

Optical label-free biosensors have demonstrated advantages over fluorescent-based detection methods by allowing accurate quantification while also being capable of measuring dynamic bimolecular interactions. A simple, high-throughput, solid-phase, and label-fr ...

Electrochemiluminescence (ECL) on bipolar electrode (BPE) is a sensitive, portable, and low-cost approach which has been employed to detect DNA and proteins. Here, we develop an ultrasensitive method for intracellular mRNA assay based on mRNA-mediated reporter DNA liberation and Ru ...

The detection of nucleic acid is of central importance for the diagnosis of genetic diseases, infectious agents, and biowarfare agents. Traditional strategies and technologies for nucleic acid detection are time-consuming and labor-intensive. Recently, isothermal strand-d ...