Pyrimidine oligonucleotides

A further unusual feature of the matrix-dependent polycondensation lies in the character of the nucleobases themselves. Purine mononucleotides undergo polycondensation, in good yields, at complementary matrices consisting of pyrimidine polymers. However, the synthesis of pyrimidine oligonucleotides from their mononucleotides at purine matrices is not effective. This important fact means that a pyrimidine-rich matrix leads to a purine-rich nucleic acid, which is itself not suitable to act as a matrix. This phenomenon also occurs when matrices are used which contain both basic species, i.e., purines and pyrimidines. An increase in the amount of purine in a matrix leads to a clear decrease in its effectiveness (Inoue and Orgel, 1983). However, the authors note self-critically that the condensation agent used cannot be considered to be prebiotic in nature. 

Dizdaroglu M, Simic MG (1985b) Radiation-induced crosslinking of pyrimidine oligonucleotides. Radiat Phys Chem 26 309-316... 

Pyrimidine oligonucleotides specific partial hydrolysate of Bacillus sublilis DNA... 

Figure 4 A triple helix formed by a pyrimidine oligonucleotide (black ribbon) covalently linked to an intercalating agent (star). The intercalating agent binds at the triplex-duplex junction and can i) stabilize the triple-helical structure (acridine derivative, 7), ii) induce double strand cleavage (phenanthroline, 12), iii) photo-induce cleavage (ellipticine derivative, 13), iv) photo-induce cross-linking of the two DNA strands (psoralen, 10).

Pancreatic RNa.se is an enzyme specific for cleavage where a pyrimidine ba.se lies to die 3 -side of die pho.sphodie.ster it acts endo. The products are oligonucleotides widi pyrimidine-3 -P04 ends ... 

CpG stands for cytosine phosphate guanine dinucleotide in a particular sequence context. CpG motifs are responsible for proliferative effects of antisense oligonucleotides, particularly with respect to B-lymphocytes. Die optimal immune-stimulatory consensus sequence surrounding CpG is R1R2CGY1Y2, where R1 is a purine (mild preference for G), R2 is a purine or T (preference for A), and Y1 and Y2 are pyrimidines (preference for T). 

The ability of o-QM to form several metastable adducts with pyrimidine (at cytosine N3) and purine bases (at guanine N7 and adenine Nl) in water suggested that the above adducts may be exploited as o-QM carriers under mild conditions, anticipating that o-QM could actually migrate along the structure of an oligonucleotide.35... 

Nucleotides can be linked together into oligonucleotides through a phosphate bridge at the 5 position of one ribose unit and the 3 position of another. The purine bases, adenine and guanine, have two heterocyclic rings, while the pyrimidines cytosine, thymine, and uracil have one. The structure of adenosine monophosphate is shown in Figure 11. 

Scheme 5 a Flavin-H-phosphonate and formacetal-linked thymine dimer phospho-ramidite used for the synthesis of the flavin and dimer containing DNA-strands 7-12. b Representation of a reduced flavin- and formacetal-linked cyclobutane pyrimidine dimer containing DNA strand, which upon irradiation (hv) and electron transfer (ET) performs a cycloreversion (CR) of the dimer unit, c Depiction of the investigated oligonucleotides... 

The liberation of the third, newly formed strand is of great importance in this process it is made possible by adding free dodecameric purine oligonucleotides, which can bond to the newly-formed pyrimidine matrix by Watson-Crick pairing. 

Figure 27.1 Three common nucleoside triphosphate derivatives that can be incorporated into oligonucleotides by enzymatic means. The first two are biotin derivatives of pyrimidine and purine bases, respectively, that can be added to an existing DNA strand using either polymerase or terminal transferase enzymes. Modification of DNA with these nucleosides results in a probe detectable with labeled avidin or streptavidin conjugates. The third nucleoside triphosphate derivative contains an amine group that can be added to DNA using terminal transferase. The modified oligonucleotide then can be labeled with amine-reactive bioconjugation reagents to create a detectable probe.

Oligonucleotides have also been separated by ion-exchange chromatography of yeast ribonucleic acid treated either with acid216 or with ribonuclease.209 Alkaline hydrolysis of the fission products obtained with the latter gives rise to pyrimidine nucleoside 3-phosphates and mixtures of purine nucleoside 2- and 3-phosphates. Bone phosphomonoesterase196 followed by alkaline hydrolysis gives pyrimidine nucleosides and purine... 

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