Words similar to abasic
Example sentences for: abasic
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P2s have two abasic residues at the 5' end to reduce primer-dimer formation (unpublished data).
A contact plot of huAPE1 with the DNA in the 1DE8 crystal structure (Figure 5) shows that motifs 1-3,5-8, and 10-12 all have residues close to the substrate, an oligonucleotide containing an abasic site (AP-DNA).
An alanine substitution mutant, N226A, of a conserved residue at the end of molego 7a that forms a hydrogen bond with the second phosphate group downstream of the abasic site, had enhanced APE activity but increased Km and Kd values, similar to an alanine mutant of R177, which binds to the same site, reported previously [ 34 ] . A combination of the two mutants, N226A and R177A, substantially reduced the ability of APE1 to bind to DNA containing an abasic site (Izumi et al.
This redundancy of binding to the 3' side is unique to APE, as is its strong binding to the DNA opposite the abasic site.
For example, Herschlag and co-workers have previously shown that a nucleobase could complement an abasic site within the hammerhead ribozyme, restoring cleavage activity [ 1 ] . Similarly, Porta and Lizardi engineered a hammerhead ribozyme that assumed an inactive secondary structure; upon the addition of an oligonucleotide that disrupted the engineered secondary structure, the ribozyme was activated [ 2 ] . More recently, it has previously been shown that many selected nucleic acid binding species (aptamers) undergo conformational changes upon ligand binding [ 3 4 5 6 ] In addition, when aptamers are conjoined to ribozymes, the ligand-induced conformational changes in the aptamers frequently modulate the structures and hence the activities of the ribozymes [ 7 8 9 ] For example, binding of theophylline to the anti-theophylline aptamer [ 10 ] modulates the conformation of residue [ 11 12 ] and the overall stability of the aptamer [ 10 13 ] . Appending the anti-theophylline aptamer to the hammerhead ribozyme allowed cleavage activity to be modulated by 110-fold by theophylline [ 13 ] . Similarly, appending the anti-theophylline aptamer to a small ribozyme ligase (L1) generated an aptazyme that was activated 1,600-fold by saturating theophylline concentrations [ 14 ] .
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