Phosphoramidite, DNA synthesis

Phosphine(s), chirality of, 314 Phosphite, DNA synthesis and, 1115 oxidation of, 1116 Phospholipid, 1066-1067 classification of, 1066 Phosphopantetheine, coenzyme A from. 817 structure of, 1127 Phosphoramidite, DNA synthesis and, 1115 Phosphoranc, 720 Phosphoric acid, pKa of, 51 Phosphoric acid anhydride, 1127 Phosphorus, hybridization of, 20 Phosphorus oxychloride, alcohol dehydration with. 620-622 Phosphorus tribromide, reaction with alcohols. 344. 618 Photochemical reaction, 1181 Photolithography, 505-506 resists for, 505-506 Photon, 419 energy- of. 420 Photosynthesis, 973-974 Phthalic acid, structure of, 753 Phthalimide, Gabriel amine synthesis and, 929... 

Incorporation of a flavin electron donor and a thymine dimer acceptor into DNA double strands was achieved as depicted in Scheme 5 using a complex phosphoramidite/H-phosphonate/phosphoramidite DNA synthesis protocol. For the preparation of a flavin-base, which fits well into a DNA double strand structure, riboflavin was reacted with benzaldehyde-dimethylacetale to rigidify the ribityl-chain as a part of a 1,3-dioxane substructure [49]. The benzacetal-protected flavin was finally converted into the 5 -dimethoxytri-tyl-protected-3 -H-phosphonate ready for the incorporation into DNA using machine assisted DNA synthesis (Scheme 5a). For the cyclobutane pyrimidine dimer acceptor, a formacetal-linked thymine dimer phosphoramidite was prepared, which was found to be accessible in large quantities [50]. Both the flavin base and the formacetal-linked thymidine dimer, were finally incorporated into DNA strands like 7-12 (Scheme 5c). As depicted in... 

The microspheres—synthesised via a two-step process (acid-catalysed hydrolysis and condensation of 3-mercaptopropyltrimethoxysilane (MPS) in aqueous solution, followed by condensation catalysed by triethanolamine)—have a narrow size distribution (Figure 5.16) and are considerably more stable than polystyrene divinylbenzene microspheres as shown in phosphoramidite oligonucleotide synthesis by the excellent retention of fluorescence intensity in each of the reagent steps involved in phosphoramidite DNA synthesis (Figure 5.17, in which the organo-silica microsphere free thiol groups are derivatized with ATTO 550 maleimide coupled to the entrapped dye). 

The phosphoramidite of 8-Ph-dG has been prepared and used to site-specifically incorporate it into oligonucleotides using solid-phase DNA synthesis. In the 12-mer 5 -d(GCGCCXGCGGTG), where X = 8-Ph-dG, the adduct behaved very similar to 8-Me-dG with of the duplex being 5.6°C lower than the normal dG dC base pair, while the of 8-Ph-dG dG was 2.1°C higher than that of the mismatched dG dC base pair. This data suggested that, similar to 8-Me-dG, 8-Ph-dG exists primarily in the anti conformation when paired with dC, while the syn conformation may pair with dGMP. ... 

DNA sequencing Maxam-Gilbert method restriction endonuclease restriction fragment palindrome Sanger dideoxy method DNA synthesis DMT ether phosphoramidite phosphite polymerase chain reaction (PCR)... 

Recently, phosphoramidite building blocks of l,iV -ethenoadenosine and 2 -deoxy-l,A( -ethenoadenosine for automated DNA synthesis have been prepared and fluorophore-labeled oligonucleotides of defined sequence have been synthesized. Almost simultaneously, guanine -1, iV -ethenoadenine base pairs were found in an oligodeoxyribonucleotide by X-ray crystallography. ... 

The occurrence at 5-( -D-glucopyranosyloxymethyl-2 -deoxyuridine ( 8dJ) in DNA, for instance of Trypanosoma brucei [180,181,182], led to the development of an efficient route for the synthesis of dJ (O Scheme 28) and its phosphoramidite as building blocks for DNA synthesis [183]. The synthesis was based on glucosyl donor 28a (R = R = Bz) which gave with acceptor 28b intermediate 28cj8 and after deprotection 8dJ. Similarly, from 28a (R = Bn, R = Ac) and 28b a-linked 28ca was obtained which led to adJ. 

RNA Synthesis. - Methods for the synthesis of RNA are now routine but less efficient than DNA synthesis. The most popular phosphoramidite reagents employ acyl protecting groups for the exocyclic amino functions of the nucleosides, dimethoxytrityl for the 5 -hydroxyl function and 2 -0-tert-butyldimethyl-silyl (tBDMS) for the 2 -hydroxyl function. The silyl protecting group is usually removed by treatment with IM TBAF or ti iethylamine.3HF. Acidic deprotection conditions have also been developed for removal of tBDMS groups. ... 

Thymidine and 2 -deoxycytidine phosphoramidite monomers have been prepared using 3 -[2-(2-nitrophenyl)propyloxycarbonyl] protecting groups, which are removed photochemically, to allow for 5 3 DNA synthesis by photolitho-... 

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