Oligonucleotides chain

Step 4 With the coupling accomplished, the phosphite product is oxidized to a phosphate by treatment with iodine in aqueous tetrahydrofuran in the presence of 2,6-dimethylpyridine. The cycle (1) deprotection, (2) coupling, and (3) oxidation is then repeated until an oligonucleotide chain of the desired sequence has been built. 

Cech and co-workers obtained a ribozyme which had been shortened via splicing, the L-19 RNA, from the system described above in the presence of guanosine or guanosine nucleotide as a cofactor, an intron with 414 nucleotides is cut out of the precursor rRNA, the result of splicing being L-19 RNA, which contains 395 nucleotides Cech was able to show that L-19 RNA is able to shorten and lengthen other oligonucleotide chains. 

Some may say at this point that proteins derive in any case from nucleic-acid templates - perhaps through a primitive genetic code. However, this is really no argument - it merely shifts the problem of the etiology of peptide chains to etiology of oligonucleotide chains, all arithmetic problems remaining more or less the same. 

T. Hianik, V. Gajdos, R. Krivanek, T. Oretskaya, V. Metelev, E. Volkov and P. Vadgama, Amperometric detection of DNA hybridisation on a gold surface depends on the orientation of oligonucleotide chains, Bioelectrochemistry, 53 (2001) 199-204. 

NRTIs are nucleoside analogues that become incorporated into the growing viral DNA chain. Once in the oligonucleotide chain, the NRTI prevents further elongation of the chain because the NRTI lacks a functional 3 -OH for attachment of the next nucleotide. Based on this mode of action, NRTIs are sometimes called chain terminators. With the synthesis of DNA severely impeded, the progress of the viral infection is slowed. 

The condensation of 3,4-HP with deoxyribonucleotide results in a unique metal-binding nucleotide (55) which can be incorporated into an oligonucleotide chain. This ohgonu-cleotide has higher thermostability in the presence of Cu(II) compared with an A-T pair, wherein Cu(II) binds to 3,4-HP from each strand to form a double helix (56). li en the Fe(II)-mimosine complex is introduced to plasmid DNA, cleavage of the supercoiled form is observed in the presence of H2O2 and dithiothreitol. The observations described in this section point to mimosine (9) and its analogues as the leads for further exploration of their potential application as metal chelators and therapeutics. 

The chemical synthesis of RNA has the distinct advantage of allowing for site-selective incorporation of modified nucleosides into the oligonucleotide chain. The early phosphodi-ester method developed by Khorana (30) was followed by the H-phosphonate and phosphoramidite approaches (31). Although the H-phosphonate approach has distinct advantages over phosphoramidite synthesis, it is not as widely used. Therefore, the focus of this section will be on the more commonly employed... 

Bis(hydroxymethyl)phosphonic acid esters that incorporated thymine were employed as a backbone to prepare short oligonucleotide chains. This chain was prepared by condensation of the bis(4,4 -dimethoxytrityl) protected phosphonic acid and iV or N -(2-hydroxyethyl)thymine in the presence of l-(2-mesitylenesul-fonyl)-3-nitro-l,2,4-triazole or by an Appel reaction with or N -(2-aminoethyl)thymine (89a-h). Selective removal of one DMT-group and phos-phitylation yielded the building blocks for solid supported synthesis of the short oligomers by the phosphoramidite approach. Holy has reported the synthesis of 8-amino and 8-substituted amino derivatives of acyclic purine nucleotide analogues. The 8-amino, 8-methylamino- and 8-dimethylamino-adenine and -guanine analogues of iV-(2-phosphonomethoxyethyl) and (S)-iV-(3-hydroxy-2-phosphono-methoxy-propyl) derivatives of purines (90a-i), were prepared by... 

Endonuclease An enzyme that hydrolyzes (breaks) an oligonucleotide chain between particular bases only consequently, the pattern of pieces of DNA (oligos) generated by the action of endonuclease on DNA of a particular organism is reproducible. 

In nature, complementary single-stranded oligonucleotide chains combine to double-stranded DNA, as a result of hydrogen binding between the A-T pairs and the G-C pairs. The typical conformation is the double-helix stracture, where the sugar-phosphates are facing outwards to solution and the more hydrophobic nucleobases facing inwards. 

Work combining MS and degradation data have also been presented. - Oxidative elimination of the polynucleotide with periodic acid cleaves the 3 -connected nucleotide chain. The terminal base thus liberated is then analyzed, and the process is repeated until the end of the sequence. Another report combined MS with enzymatic digestion data, in particular, the selective cleavage by venom phosphoesterase of the oligonucleotide chain from the 3 end. The separation of nucleotides on a Dowex column and subsequent derivatization leads to the determination of both 5 and 3 terminal nucleotides according to Scheme 1. 

The early attempts to use relatively easily available diastereomerically pure nucleoside 3 -0-(2-cyanoethyl-AT,AT-diisopropylphosphoramidite) monomers for the stereospecific synthesis of PS-Oligos failed because of inevitable racemiza-tion of Pm intermediate caused by an excess of lff-tetrazole necessary for efficient elongation of oligonucleotide chain [13]. An idea to use for that purpose appropriately protected nucleosides functionalized at 3 -0 position with 2-thio-1,3,2-oxathiaphospholane moiety arose from the studies on the reactions of di-substituted phosphorothioates with oxiranes [14,15], and in particular from the observation that PS-PO exchange in 0,0-diphenyl phosphorothioate (8) upon treatment with ethylene oxide in methanol solution resulted in formation of... 

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