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In Vivo Chromatin Decondensation Assays: Molecular Genetic Analysis of Chromatin Unfolding Characteristics of Selected Proteins

Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the i ...

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Analysis of Reconstituted Chromatin Using a Solid-Phase Approach

Complex experimental strategies involving in vitro reconstituted chromatin or simple chromatin interaction studies are much facilitated by immobilizing the nucleosomal arrays to paramagnetic beads. Chromatin-containing beads can be retrieved from a reaction mix solut ...

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DNA Methyltransferase Probing of Chromatin Structure Within Populations and on Single Molecules

Non-invasive methods for mapping chromatin structure are necessary for creating an accurate view of genome function and dynamics in vivo. Ectopic induction of cytosine-5 DNA methyltransferases (C5 MTases) in Saccharomyces cerevisiae is a powerful technique for probing chromat ...

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Visualization of the Expression of HMGN Nucleosomal Binding Proteins in the Developing Mouse Embryo and in Adult Mouse Tissues

Visualization of the expression pattern of specific proteins during development and in adult tissues provides important clues as to their possible role in various cellular processes. Mouse is the organism of choice for obtaining information on gene expression patterns in higher euk ...

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Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin

Chromosome analysis is a fundamental technique for cytogenetic studies. Chromosomes are conventionally prepared from mitotic cells arrested by colcemid block protocol. However, obtaining the mitotic chromosomes is often hampered under several circumstances. As a result, c ...

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Preparation and Analysis of Uniquely Positioned Mononucleosomes

Short DNA fragments containing single, uniquely positioned nucleosome cores have been extensively employed as simple model experimental systems for analysis of many intranuclear processes, including binding of proteins to nucleosomes, transcription, DNA repair and ATP-d ...

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Analysis of DNA Topology in Yeast Chromatin

Topology of closed circular DNA is affected by its packaging into nucleosomes and potentially by alteration of nucleosome structure. Changes in topology that reflect alterations in chromatin structure can be measured and quantified using closed circular plasmids from living yea ...

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Monitoring DNA Breaks in Optically Highlighted Chromatin in Living Cells by Laser Scanning Confocal Microscopy

The recognition and repair of DNA lesions occurs within a chromatin environment. Genetically tagging fluorescent proteins to DNA damage response proteins has provided spatial and temporal details concerning the establishment of biochemical subnuclear regions geared towa ...

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Differential Display Using Random Hexamer-Primed cDNA, Motif Primers, and Agarose Gel Electrophoresis

Polypeptide growth factors stimulate cellular proliferation by binding to the extracellular domain of transmembrane receptors and thereby activating intracellular signal transduction pathways. One cellular response to mitogenic stimulation is the sequential tran ...

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Fingerprinting by Arbitrarily Primed PCR

PCR using primers of arbitrary sequence can generate a reproducible fingerprint of products from DNA (1,2). Differences in the fingerprint of products generated from DNA of related organism are a result of polymorphisms. These polymorphisms proved useful markers for genetic mapping ( ...

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Fluorescent Differential Display

Since their first introduction in 1992 (1,2), differential display (DD) and its relatives have been used extensively in various fields of biology where the identification of differentially expressed messages are of particular interest and importance (for review, see ref. 3). These new te ...

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Cloning Differentially Expressed Genes by Using Differential Display and Subtractive Hybridization

Differential gene expression occurs in all phases of life, including development, maintenance, injury, and death of an organism. Being able to identify these genes will help understand not only gene function but also the underlying molecular mechanisms of a particular biological syst ...

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A Direct-Sequencing-Based Strategy for Identifying and Cloning cDNAs from Differential Display Gels

This report describes an approach to identifying and cloning messages from differential display (DD) gels that has markedly reduced the occurrence of false positives as well as the time required for the process. Most importantly, the use of Northern blots with potentially contaminated p ...

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Direct Sequencing of Differential Display PCR Products

The polymerase chain reaction (PCR)-based mRNA differential display (1) has become an increasingly popular alternative technique for isolating genes of interest in a variety of in vitro and in vivo systems (for review, see ref. 2), as compared to such conventional techniques as differenti ...

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Differential Screening of Differential Display cDNA Products by Reverse Northern

Differential Display (DD) is a widely used methodology for cloning differentially expressed genes. Since its inception in 1992 (1), much effort has been made to improve and optimize the technique (2,3). One major bottle-neck remains, though, in the screening step for the verification of the cDNA ...

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Screening for Positive Clones Generated by Differential Display

Differential display is a powerful method to identify genes that are differentially expressed in different tissues or in the same tissue exposed to different treatments (1,2). The method can be performed with relatively little biological material, and the resulting partial cDNAs can be c ...

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RC4DRestriction Fragment Length Polymorphism-Coupled Domain-Directed Differential Display

Since many life processes, such as development and reproduction, depend on differential gene expression, the spatiotemporal pattern of gene expression is of prime biological interest. Accordingly, the concepts of the mRNA differential display (DD) and RNA fingerprinting techni ...

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Cloning of the 3 Noncoding Regions from Several Members of Heat Shock Protein Gene Families by Differential Display

Several structural and metabolically important proteins in eukaryotes are encoded by multigene families. For understanding the function of each member of a gene family, it is essential to isolate the representative cDNAs encoding the protein of interest. In the past, this has been especi ...

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Identification of ImmediateEarly Gene Targets of the Raf-1 Serine/Threonine Protein Kinase Using an Estradiol-Dependent Fusion Protein, Raf-1:ER

The Raf-1 serine/threonine protein kinase is a central component of the Ras/Raf/MEK/MAP kinase cascade, a highly conserved signaling pathway responsible for the transmission of signals emanating from cell surface growth factor, cytokine, and hormone receptors into the nucleus (1–4 ...

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Isolation of Cytokine-Inducible Genes from Hematopoietic Cells by Differential Display

Hematopoietic stem cells have the capacity to divide and differentiate into several different hematopoietic cell lineages. Hematopoietic growth factors (cytokines) promote both the growth and differentiation of stem cells and committed progenitor cells. Cytokines bind and ...

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