Oligonucleotides cleavage

While considerable effort has been devoted to generating chemical modifiers for DNA and rna, a consensus opinion has emerged in recent years that selective oligonucleotide cleavage may best be accomplished in an antisense (i.e., directed) fashion using either chemically enhanced hydroly-gjg162,183,189-193 absorption-triggcred photolysis.As it currently... 

Photolabile CPG supports, based on the ort/io-nitrobenzyl moiety, have been designed by Greenberg et al. [118,119] to provide orthogonal oligonucleotide cleavage conditions suitable for alkali-sensitive oligonucleotides. 

Kwiatkowski M, Nilson M, Landegren U. Synthesis of full-length oligonucleotides Cleavage of apurinic molecules on a novel support. Nucl Acids Res... 

Roupioz Y, Lhomme J, Kotera M. Chemistry of the 2-deoxyribonolactone lesion in oligonucleotides cleavage kinetics and products analysis. J Am Chem Soc. 2002 124 9129-9135. 

Finally, in 2007, the Reinhoudt and Ungaro groups made the step to RNA oligonucleotide cleavage by their di- and trinuclear Cu(II) complexes of [12] aneNs macrocycles anchored at the upper rim of calix[4]arenes (e.g., 76, Fig. 24.28). All complexes were found to cleave 6-, 7-, and 17-meric oligonucleotides. Enzyme-like kinetics were established in electrophoretic assays with P-labeled phosphates in the terminal 5 -position. Remarkably, all metal complexes strongly preferred the CpA sequence over other dinucleotides, similar to ribonu-clease A. The trinuclear Cu(II) complex almost reached a million-fold rate enhancement [90]. 

Artificial endonucleases, ie, molecules able to cleave double-stranded DNA at a specific sequence, have also been developed. These endonucleases can be obtained by attaching a chemically reactive group to a sequence-specific oligonucleotide. When the oligonucleotide is bound to its complementary sequence, the activation of the reactive group results in double-stranded DNA cleavage. 

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 ... 

Cleavage of oligonucleotide from solid support and removal of A benzoyl and A isobutyryl blocking groups. 

Bu4N F , THF, Pyr, H2O, rt, 30 min. These conditions result in the formation of a mixture of fluorophosphate and phosphate. In the case of oligonucleotides, some intemucleotide bond cleavage is observed with this reagent. 

As we have already seen zinc-finger peptides are well-studied polypeptide motifs that have found many applications in synthetic systems, mostly because of their abihty to bind metal ions and interact with oligonucleotides. In this context the report by lima and Crooke [44] of the hydrolytic cleavage by a zinc-finger peptide devoid of any metal ion is a surprising. The system they studied, a 30-amino acid sequence, is based on a catalytic mechanism very similar to that discussed above... 

---