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Aminopeptidases: Aminopeptidase M (EC 3.4.11.2), Pyroglutamate Aminopeptidase (EC 3.4.19.3), and Prolidase (EC 3.4.13.9)

Aminopeptidases are proteolytic enzymes that remove L-amino acids sequentially from the amino termini of polypeptide chains. A number of aminopeptidases have been isolated, including leucine aminopeptidase from serine kidney cytosol (1), aminopeptidase P from E. coli (2), proli ...

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Alkaline Phosphatase (EC 3.1.3.1)

Alkaline phosphatases (or alkaline phosphomonoesterases) catalyze the hydrolysis of phosphate monoesters of a variety of alcohol moieties, being most active at an alkaline pH. The enzymes have been isolated from a variety of sources, including bacteria, fungi, invertebrates, fish, ...

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Nucleases: An Overview

Enzymes able to digest nucleic acids are of course essential to molecular biology, indeed the whole technology was founded on the discovery of bacterial enzymes that cleave DNA molecules in a base-specific manner. These enzymes, the type II restriction endonucleases, are perhaps the best s ...

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Polynucleotide Kinase (EC 2.7.1.78)

The enzyme polynucleotide kinase (PNK, or ATP:5′-dephospho-polynucleotide 5′-phosphatase) catalyzes the transfer of a γ-phosphate group from a 5′-nucleoside triphosphate moiety to a free 5′-hydroxyl of a polynucleotide such as DNA or RNA, to form a 5′-phosphorylated DNA or RNA molecule a ...

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Deoxyribonuclease I (EC 3.1.21.1) and II (EC 3.1.22.1)

From Chapter 1 on nucleases, we know that the term DNase refers to an enzyme that endonucleolytically cleaves DNA molecules. This chapter deals with those DNases that preferentially catalyze the hydrolysis of double-stranded DNA (ds DNA) and that have found a use in the various techniques empl ...

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Taq Polymerase (EC 2.7.7.7): With Particular Emphasis on Its Use in PCR Protocols

Taq polymerase (EC 2.7.7.7) is a thermostable DNA-dependent DNA polymerase that was first isolated in 1976 from Thermus aquaticus strain YT-1 (ATTC # 25 104)(1). It catalyzes the template-directed polymerization of dNTPs at high temperatures. When Taq polymerase was isolated in 1976, nobody ...

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DNA Polymerases (EC 2.7.7.7)

DNA polymerases catalyze the synthesis of DNA molecules from monomeric deoxynucleotide triphosphate units. This definition encompasses those enzymes classed as DNA-dependent DNA polymerases (EC 2.7.7.7, which require both a DNA template strand and a DNA primer to which the monomer ...

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Eukaryotic Nuclear RNA Polymerases (EC 2.7.7.6)

DNA-dependent RNA polymerases (ribonucleoside triphosphate: RNA nucleotidyltransferase, EC 2.7.7.6) catalyze the synthesis of RNA from ribonucleoside triphosphates in the presence of a DNA template and divalent cation (1).

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Reverse Transcriptase (EC 2.7.7.49): The Use of Cloned Maloney Murine Leukemia Virus Reverse Transcriptase to Synthesize DNA from RNA

The conversion of mRNA into cDNA is the essential first step in the study of eukaryotic cell products expressed from cloned genes. The key enzyme used first in this process, retroviral RNA-directed DNA polymerase (reverse transcriptase), catalyzes the synthesis of a DNA copy of an RNA template in ...

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Terminal Deoxyribonucleotidyl Transferase (EC 2.7.7.31)

Terminal deoxyribonucleotidyl transferase (TdT) (EC 2.7.7.3 1) catalyzes the addition of deoxynucleoside triphosphates to the 3′ ends of oligo-and polynucleotide primers. Different from all the other known DNA polymerases, TdT-catalyzed DNA synthesis is not template-direct ...

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Restriction Enzymes

Restriction enzymes are endonucleases that recognize specific double-stranded DNA sequences and cleave the DNA in both strands, e.g.: (1) They have been identified in many prokaryotic organisms and are considered to be part of a defense system directed against foreign DNA. Site-specific ...

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DNA Methyltransferases (EC 2.1.1.72 and EC 2.1.1.73)

DNA methyltransferases (Mtases) catalyze the transfer of the S-methyl group of S-adenosylmethionine (SAM) to deoxycytosine (dC) or deoxyadenine (dA) bases within defined DNA sequences (1). Individual enzymes are specific for one or the other base, and modify at the 6-NH2 of dA (EC 2.1.1.72) or at t ...

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CDK Pathway: Cyclin-Dependent Kinases (cdks) and Cyclin-Dependent Kinase Inhibitors

In elucidating a novel cell-cycle pathway or mode of regulation, it will first be necessary to establish that the cell is arrested in a particular stage of the cell cycle following arrest-inducing conditions. This is achieved by staining the DNA in a population of cells with propidium iodide and then ...

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Developmental Biology Protocols: Overview II

The discipline of developmental biology covers scientific investigations aimed at deciphering the underlying mechanisms responsible for diversity and order within tissues and organs. It is the goal of Developmental Biology Protocols to present to the readers a set of contempora ...

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Retroviral Infection of T-Cell Precursors in Thymic Organ Culture

The ex vivo culture of intact fetal thymus lobes, fetal thymic organ culture (FTOC) has proven to be a useful technique for the elucidation of the molecular and cellular bases of T-cell development and T-cell receptor (TCR) repertoire selection (reviewed in ref. 1. Most dramatically, FTOC has been u ...

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Skin Morphogenesis: Embryonic Chicken Skin Explant Cultures

Chicken skin development is an excellent model to study the mechanisms of morphogenesis. It has a long experimental history and has been well characterized phenotypically. Chicken skin offers distinct patterns, large numbers of different cutaneous appendages, availability of in v ...

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Assay for the Isolation of Hepatogenic Factors: Key Molecules in Hepatocyte Formation and Liver Morphogenesis

During embryonic development, pluripotent cells from the endoderm layer are directed toward specific cell lineages, leading to the formation of highly specialized organs, such as liver, lung, and pancreas. In case of liver, hepatocyte specification and maturation is the result of a tiss ...

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Apoptosis in Development

Development involves a delicate orchestration of cell division, movement, differentiation, and death. Cell death in mammalian embryogenesis occurs as early as inner cell-mass differentiation, and it continues to be part of the developing embryo during the formation and functional ...

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Methods to Detect Patterns of Cell Death in Drosophila

There are many times during Drosophila development or in the adult when cell death contributes to a phenotype of interest (e.g., refs. 1-5, and many others). The cell death may be primary to gene function or a secondary consequence of failure of proper differentiation or cell maintenance (e.g., ref. 6). To d ...

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Drosophila as a Genetic Tool to Define Vertebrate Pathway Players

In many instances, the strength of Drosophila melanogaster genetics can be used to enhance our understanding of complex vertebrate signaling systems. The general success of this approach is underscored by the large number of vertebrate signaling components whose very names derive in p ...

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