Oligonucleotides, laboratory synthesis

The laboratory synthesis of oligonucleotides and polynucleotide fragments is a subject of great importance. Much has already been acheived (Chapter 10.4C). In addition to hydrolysis, however, the nucleic acids are very sensitive to a wide range of chemical reactions, for example, the heterocyclic bases are subject to alkylation, oxidation and reduction. Generally only mild reactions can be used in the construction of an oligonucleotide chain... 

The triphenylmethyl, or trityl, ether (-CPha, or Tr) can be cleaved by reduction or with acid, via the stabilized trityl carbocation. Derivatives of the trityl group are widely used as protective groups in the laboratory synthesis of oligonucleotides (DNA). 

Combinatorial Hbraries are limited by the number of sequences that can be synthesized. For example, a Hbrary consisting of one molecule each of a 60-nucleotide sequence randomized at each position, would have a mass of >10 g, weU beyond the capacity for synthesis and manipulation. Thus, even if nucleotide addition is random at all the steps during synthesis of the oligonucleotide only a minority of the sequences can be present in the output from a laboratory-scale chemical DNA synthesis reaction. In analyzing these random but incomplete Hbraries, the protocol is efficient enough to allow selection of aptamers of lowest dissociation constants (K ) from the mixture after a small number of repetitive selection and amplification cycles. Once a smaller population of oligonucleotides is amplified, the aptamer sequences can be used as the basis for constmcting a less complex Hbrary for further selection. 

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 scientific world was amazed to hear that David Lee, from the laboratory of Reza Ghadiri (Scripps Research Institute, La Jolla, California), had found a self-replicating peptide (Lee et al., 1996) there are analogies to the experiments with oligonucleotides (see Sect. 6.4). Lee was able to show that a certain peptide, containing 32 amino acids, can both function as a matrix and also support its own synthesis autocatalytically. The information transfer is clearly more complex than that involved in nucleic acid replication. In the case of this particular peptide, both the... 

William Fraser was born in Hamilton. He studied at the other of the two local universities, Strathclyde, where he obtained a first class B.Sc. honors degree in 1986 and Ph.D. in 1989 under the direction of Professor Colin J. Suckling and Professor Hamish C. S. Wood. He was awarded a Royal Society European Exchange Postdoctoral Fellowship and worked in the laboratories of Professor Albert Eschenmoser at the ETH, Zurich. In 1991, he took up his present position as lecturer in medicinal chemistry at Aston University, Birmingham. His scientific interests include nucleoside and nucleic acid chemistry, solid-supported, synthesis, and study of base-modified antigene oligonucleotides targeted to DNA. 

In Vitro. In our laboratory, we have evaluated the toxicities of scores of phosphorothioate oligodeoxynucleotides in a significant number of cell lines in tissue culture. As a general rule, no significant cytotoxicity is induced at concentrations below 100 jllM oligonucleotide. Additionally, with a few exceptions, no significant effect on macromolecular synthesis is observed at concentrations below 100(188,192). 

Simultaneously, numerous academic groups started and even reoriented their activities towards the implantation of solid-phase strategies in their laboratories. Although progress towards fulfillment of the initial great expectations has slowed in recent years, solid-supported chemistry is now a very useful tool in all modern organic chemistry laboratories [11] and, of course, is the method of choice for both research and industrial synthesis of peptides [12] and oligonucleotides [13]. 

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