Oligonucleotides chemical synthesis

Enrichment of high affinity candidates is usually achieved in 8 to 15 rounds of SELEX. Each rotmd takes approximately 2 days to perform. The process has been automated using robotic liquid handlers both for DNA (SomaLogic) and RNA aptamers (Cox, 2002). Next, the sequenced aptamer is prepared in bulk by conventional DNA synthesis chemistry and purified, then the aptamer arrayed onto a solid support. Thus, an aptamer is ready for application within 2 to 3 mo. Because the sequence is known, preparation of additional aptamer is easily accomplished using conventional oligonucleotide chemical synthesis. 

It is notable that small peptides were retained on a cross-linked PEI column [37] but polypeptides over 20 residues were weakly retained or not at all. Possibly, small peptides were able to penetrate into the depth of the bonded phase while larger peptides could not. These packings were more useful for the separation of oligonucleotides, i.e. more acidic compounds. Lawson et al. [39] have shown the applicability of PEI-silicas for assessing the purity of precursor blocks, monitoring the chemical synthesis and isolating reaction products after synthesis. 

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-... 

Recent developments in DNA/RNA chemical synthesis have allowed us to attach some functional groups covalently to nucleic acids, thus permitting the introduction of a functionality or properties not normally present in the native biomolecule The use of non-nucleosidic linkers is probably the most popular approach for the 5 -terminal modification of chemically synthesized nucleic acid oligonucleotides and a number of such linkers are commercially available. The linker shown in Fig. 2 is designed as a phosphoramidate derivative so that it can be incorporated into the 5 -terminus of the sequence as the last... 

Synthetic oligonucleotides are very important tools in the study and manipulation of DNA, including such techniques as site-directed mutagenesis and DNA amplification by the polymerase chain reaction. The techniques for chemical synthesis of oligonucleotides are highly developed. Very efficient automated methodologies based on solid phase synthesis are used extensively in fields that depend on the availability of defined DNA sequences.52... 

In contrast to the biopharmaceuticals discussed thus far (recombinant proteins and gene therapy products), antisense oligonucleotides are manufactured by direct chemical synthesis. Organic synthetic pathways have been developed, optimized and commercialized for some time, as oligonucleotides are widely used reagents in molecular biology. They are required as primers, probes and for the purposes of site-directed mutagenesis. 

The Reformatsky type of reaction with Zn(0) was performed in situ and led to somewhat unstable phosphonodiamidite (step a) which was coupled with 5 -DMTr-thymidine to give the intermediate mononucleoside phospho-noamidite (step b). The latter was further coupled with 3 -acetyl-thymidine (step c). Couplings described in steps b and c were activated by tetrazole. The intermediate dinucleoside phosphonite was oxidized with (lS)-(+)-(10-camphorsulphonyl)oxaziridine (step d) or sulfurized with Beaucage reagent. The phosphonoamidites mentioned above were used in the solid-phase chemical synthesis of phosphonoacetate and thiophosphonoacetate oligonucleotides. 

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. 

P2 In this study, we report the chemical synthesis and functionalization of magnetic and gold-coated magnetic nanoparticles and the immobilization of single-stranded biotinylated oligonucleotides onto these particles. (From Kouassi and Irudayaraj, 2006)... 

Antisense oligonucleotides manufactured by direct chemical synthesis Yes No No... 

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. 

Frank, R., Heikens, W., Heisterberg- Moutsis, G. and Blocker, H., A new general approach for the simultaneous chemical synthesis of large numbers of oligonucleotides segmental solid supports, Nucl. AcidsRes., 1983,11, 4365-4377. 

The chemical synthesis of short oligonucleotides of known sequence provided a way out of the dilemma. First,... 

Muller E, Gasparutto D, Cadet J (2002) Chemical synthesis and biochemical properties of oligonucleotides that contain the (5 S,5S,6S)-5 6-cyclo-5-hydroxy-5,6-dihydro-2 -deoxyuridine DNA lesion. ChemBioChem 3 101-109... 

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