Nucleotides chemical synthesis

Frederich, M., Delvaux, D., Gigliobianco, T., Gangolf, M., Dive, G., Mazzucchelli, G., Elias, B., De Pauw, E., Angenot, L., Wins, P., and Bettendorlf, L., 2009. Thiaminylated adenine nucleotides. Chemical synthesis, structural characterization and natural occurrence. FEES Journal. TIC. 3256-3268. 

In the human cell there are 23 pairs of chromosomes containing approximately 3000 million base pairs of DNA. Short sequences of DNA, perhaps with as few as 20 nucleotide units and sometimes radiolabeled, can be obtained either by chemical synthesis (gene machine) or from cloning. These short sequences can be used to probe for a complementary sequence by looking for the position to which they bind to any DNA sample under investigation, from blood for example. Such probes can detect as little as 100 fg of DNA and are the basis of forensic genetic fingerprinting tests. 

It is now known that each codon consists of a sequence of three nucleotides ie, it is a triplet code (see Table 38—1). The deciphering of the genetic code depended heavily on the chemical synthesis of nucleotide polymers, particularly triplets in repeated sequence. 

The automated chemical synthesis of moderately long oligonucleotides (about 100 nucleotides) of precise sequence is now a routine laboratory procedure. Each synthetic cycle takes but a few minutes, so an entire molecule can be made by synthesizing relatively short segments that can then be ligated to one another. Oligonucleotides are now indispensable for DNA se-... 

The polymerase chain reaction (PCR) is an important procedure in genetic engineering that allows any DNA segment to be replicated (amplified) without the need for restriction enzymes, vectors, or host cells (see p. 258). However, the nucleotide sequence of the segment has to be known. Two oligonucleotides (primers) are needed, which each hybridize with one of the strands at each end of the DNA segment to be amplified also needed are sufficient quantities of the four deoxyribonucleo-side triphosphates and a special heat-tolerant DNA polymerase. The primers are produced by chemical synthesis, and the polymerase is obtained from thermostable bacteria. 

Selected entries from Methods in Enzymology [vol, page(s)] Determination of FMN and FAD by fluorescence titration with apoflavodoxin, 66, 217 purification of flavin-adenine dinucleotide and coenzyme A on p-acetoxymercurianiline-agarose, 66, 221 a convenient biosynthetic method for the preparation of radioactive flavin nucleotides using Clostridium kluyveri, 66, 227 isolation, chemical synthesis, and properties of roseoflavin, 66, 235 isolation, synthesis, and properties of 8-hydroxyflavins, 66, 241 structure, properties and determination of covalently bound flavins, 66, 253 a two-step chemical synthesis of lumiflavin, 66, 265 syntheses of 5-deazaflavins, 66, 267 preparation, characterization, and coenzymic properties of 5-carba-5-deaza and 1-... 

Methods of Chemical Synthesis of Amino Acid and Peptide Esters of Nucleosides, Nucleotides, and Oligonucleotides T. L. Tsilevich, A. A. Kraevskii and B. P. Gottikh, Russ. Chem. Rev. (Engl. Transl.), 1972, 41, 822-832. 

Timmons SC, Jakeman DL (2007) Stereoselective chemical synthesis of sugar nucleotides via direct displacement of acylated glycosyl bromides. Org Lett 9 1227... 

The component RNA chains may alternatively be generated by in vitro transcription, in which case the shorter helices may be replaced with short stem-loops—indeed, there is no reason why the individual species cannot be made as a single RNA transcript. The main drawback to this approach is that nonnatural nucleotides cannot be introduced, and for this chemical synthesis is essential. 

The labeling must be specific, that is, directed to a specific site in the RNA to yield meaningful results pertaining to specific nucleotides. This is commonly referred to as site-directed spin-labeling (SDSL) (Altenbach et ah, 1989 Barhate et ah, 2007 Edwards et ah, 2001 Kim et ah, 2004 Qin et ah, 2001, 2003 Schiemann et ah, 2004). Therefore, incorporation of multiple labels through enzymatic RNA synthesis (e.g., triphosphate polymerization with polymerases Keyes et ah, 1997) is of limited value. Instead, labels are generally introduced chemically, either during chemical synthesis of the nucleic acid or by postsynthetic modification of the polymer. 

The nucleotide diphosphates can be obtained by different approaches. Chemical synthesis provides an attractive route to these activated... 

The chemical synthesis involves a lot more selective manipulation of functional groups, particularly by protection, than is necessary in the biological synthesis. However, this synthesis paved the way to the simple syntheses of nucleotides and polynucleotides carried out routinely nowadays. The usual method is to build short runs of nucleotides and then let the enzymes copy them—a real partnership between biology and chemistry. 

The Chemical Synthesis of Oligo- and Pbly-nucleotides by the Phosphodies-ter Approach. Reese, C. B. Tetrahedron 1978, 34, 3143-3179. 

These early contributions were later supplemented by a comprehensive article on the mononucleotides by Ueda and Fox.4 The present article is an extension of these articles to chemical synthesis of oligo-and poly-nucleotides, and it is hoped that, in conjunction with the earlier articles, it will provide the organic chemist with a reasonable appreciation of some of the challenges, both past and present, of the synthetic chemistry of the nucleic acids. 

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