生物化学技术

RNA interference (RNAi) is now established as a general method to silence gene expression in a variety of organisms. Double-stranded RNA (dsRNA), when introduced to cells, interferes with the expression of homologous genes, disrupting their normal function. In mammals, transient deli ...

The C-terminal repeat domain (CTD) of the largest subunit of RNA polymerase II is hyperphosphorylated during transcription elongation. The phosphoCTD is known to bind to a subset of RNA processing factors and to several other nuclear proteins, thereby positioning them to efficiently ca ...

We have developed an in vivo reporter of alternative splicing decisions that allows for the determination of FGF-R2 splicing patterns without the destruction of cells. This method has broad applications, including the study of other alternatively spliced genes in tissue culture and in w ...

The ability to isolate native ribonucleoprotein (RNP) particles is of fundamental importance in the study of processes such as pre-messenger RNA (mRNA) processing and translation. We have developed an RNA affinity tag that allows the large-scale preparation of native spliceosomes in a ...

In this work we describe methods for the analysis of RNAs that have been edited by the double-strand RNA-specific adenosine deaminase, ADAR. These RNAs contain inosine residues that can be detected and quantified by a variety of approaches, including base hydrolysis and thin-layer chromat ...

Single-strand conformational polymorphism analysis has been used successfully to identify single nucleotide changes within sequences based on the fact that multidetection enhancement gels will separate molecules based on their conformation rather than their size. We have e ...

This chapter describes a simple method for the analysis of nuclear messenger RNA (mRNA) export in human cells in culture. The assay described relies on the observation that mRNA molecules containing an intron are generally retained in the nucleus until splicing is completed. Upon sequestr ...

The nuclear membrane is the defining feature of eukaryotes. It divides the cell into two functionally specialized compartments, and it is widely assumed that translation is restricted to only one: the cytoplasm. However, recent results suggest that some translation takes place in nuclei ...

The evolutionarily conserved DExD/H-box proteins are essential for all RNA-related biological processes. They are thought to modulate the structure and function of specific RNAs and/or ribonucleoprotein particles by using their intrinsic RNA-dependent ATPase activities to ...

Tandem mass spectrometry has been used for determinations of enzyme activities in biological samples. Activities in rehydrated dried blood spots of lysosomal enzymes glucocerebrosidase, acid sphingomyelinase, galactocerebroside β-galactosidase, acid-α-galacto ...

There is intense interest in determining the absolute abundance of specific proteins in complex mixtures, for example in the area of disease biomarker discovery. We have developed a set of protein-tagging reagents called visible isotope-coded affinity tags (VICAT reagents) that con ...

Over the last few years, new proteomics methods have been developed for making quantitative comparisons using stable isotope labeling. Although these methods have paved the way for quantitative proteomics, the analysis of these data is often the rate-limiting step. In fact, many analyzes ...

Metabolic labeling of mammalian organisms with stable isotopes can be used to provide tissue-specific internal standards for use in quantitative proteomic analyses. This method provides an alternative and complementary strategy to covalent modification approaches using i ...

Receptor tyrosine kinases receive extracellular cues, such as ligand binding, and transmit this information to the cell through both autophosphorylation and phosphorylation of tyrosine residues on selected substrates, stimulating a variety of signal transduction pathwa ...

Mass spectrometry-based relative quantification of proteins is often achieved by the labeling of two samples with isotopically light and heavy reagents. The intensities of the ions with different masses, but same chemical properties, can be reliably used for determining relative qu ...

One of the primary goals of proteomics is the description of the composition, dynamics, and connections of the multiprotein modules that catalyze a wide range of biological functions in cells. Mass spectrometry (MS) has proven to be an extremely powerful tool for characterizing the composi ...

Mass spectrometry (MS)-based quantitative proteomics is an increasingly popular approach to study changes in protein abundances in biological samples. Stable isotope labeling by amino acids in cell culture (SILAC), one of the more widely used methods for quantitative proteomics, is a ...

We describe a new method for quantitative tissue proteomics using culture-derived isotope tags (CDIT), which are cells grown in stable isotope-enriched medium and added to each tissue sample to provide internal standards. After protein identification by mass spectrometry (MS), each ...

The absolute quantification (AQUA) strategy provides a means to determine the precise protein or modified protein levels directly from cells or tissues. The technique is based on two major principles: stable isotope dilution theory and the use of synthetic peptides containing such sta ...

We demonstrate the quantification capability and robustness of a new integrated liquid chromatography-mass spectrometry (LC-MS) approach for large-scale profiling of proteins and metabolites. This approach to determine differential expression relies on linearity of si ...