2 -deoxyribonucleoside-5 -triphosphate dNTP

The common denominators of RNRs are radical chemistry involving redox active cysteines (see sections 3.1 and 3.3) and with few exceptions an allosteric control mediated by deoxyribonucleoside triphosphates (dNTPs) and ATP (Reichard, 1997). Yet, several other characteristics distinguish the three RNR classes (Table 1) from each other ... 

A 2 deoxyribonucleoside triphosphate (dNTP) A 2, 3 "dideoxyribonucleoside triphosphate (ddNTP) ... 

The substrates for DNA synthesis are a 3 primed site and deoxyribonucleoside triphosphate (dNTP) (see Fig. 1). DNA polymerase catalyzes a phosphoryl transfer reaction that adds a dNMP moiety to a 3 terminus of an existing DNA strand, releasing pyrophosphate (Fig. la). The reaction is catalyzed exclusively by two metal ions (e.g., Mg++) (11, 12). Metal ion A extracts a proton from the DNA primer 3 terminal hydroxyl group to produce a oxyanion nucleophile, which attacks... 

I A small piece of DNA called a primer, wdiose sequence is complementary to that on the 3 end of the restriction fragment I The four 2 -deoxyribonucleoside triphosphates (dNTPs)... 

The adenosylcobalamin-dependent RTPR catalyzes the reduction of ribonucleoside triphosphates (NTPs) to deoxyribonucleoside triphosphates (dNTPs) for DNA biosynthesis according to Equation (18). 

Most of the carbon that flows through nucleotide synthetic pathways goes into ribonucleotide triphosphates (rNTPs - ATP, CTP, GTP, and UTP). A relatively small fraction is diverted to the synthesis of deoxyribonucleoside triphosphates (dNTPs). rNTPs are synthesized in excess of dNTPs because most cells contain 5-10 times as much RNA as DNA and because rNTPs have multiple metabolic roles, whereas dNTPs are used only to make DNA. 

The DNA to be sequenced is mixed with a short oligonucleotide that serves as a primer for synthesis of the complementary strand. The primer is hydrogen-bonded toward the 3 end of the DNA to be sequenced. The DNA with primer is divided into four separate reaction mixtures. Each reaction mixture contains all four deoxyribonucleoside triphosphates (dNTPs), one of which is labeled to allow the newly synthesized fragments to be visualized by autoradiography or by fluorescence, as described in Section 13.1. In addition, each of the reaction mixtures contains one of the four ddNTPs. Synthesis of the chain is allowed to proceed in each of the four reaction mixtures. In each mixture, chain termination occurs at all possible sites for that nucleotide. 

The basics of chemistry for the synthesis of DNA by the polymerization of deoxyribonucleoside triphosphates (dNTP) involve condensation of dNTPs or oligo-dNTP and dNTP monomer by phosphodiester linkages and maintenance of the chain elongation process to obtain the final DNA with specific numbers of nucleotides in specific sequences and appropriate base pairing through hydrogen bonds. 

The essential feature of DNA synthesis is the formation of a phosphodiester linkage between a growing 5 -3 DNA strand and an incoming dNTP (deoxyribonucleoside triphosphate). The bond is created by a nucleophilic attack of the 3 -hydroxyl group of the terminal residue on the a-phosphate of the dNTP. 

DNA replication uses deoxyribonucleoside-5 -triphosphates (dNTPs) to build the DNA chains. 

RGURE 8-39 Nucleoside phosphates General structure of the nucleoside 5 -mono-, di-, and triphosphates (NMPs, NDRs, and NTRs) and their standard abbreviations In the deoxyribonucleoside phosphates (dNMPs, dNDPs, and dNTPs), the pentose is2 -deoxy-D-ribose. 

The ribonucleoside di- and triphosphates (NDPs, NTPs) and deoxyribonucleoside di- and triphosphates (dNDPs, dNTPs) have important functions in the cell. They operate as energy carriers in various reactions and as precursors for the synthesis of nucleic acids (Chaps. 10 and 16). 

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