Covalent Schiff base catalysis and turnover by a DNAzyme: a M2+ -independent AP-endonuclease mimic.
A DNAzyme, synthetically modified with both primary amines and imidazoles, is found to act as a M2+ -independent AP lyase-endonuclease. In the course of the cleavage reaction, this DNAzyme forms a covalent Schiff base intermediate with an abasic site on a complementary oligodeoxyribonucleotide. This intermediate, which is inferred from NaCNBH3 trapping as well as cyanide inhibition, does not evidently accumulate because the second step, dehydrophosphorylative elimination, is fast compared to Schiff base formation. The 5'-product that remains linked to the catalyst hydrolyzes slowly to regenerate free catalyst. The use of duly modified DNAzymes to perform Schiff base catalysis demonstrates the value of modified nucleotides for enhancing the catalytic repertoire of nucleic acids. This work suggests that DNAzymes will be capable of catalyzing aldol condensation reactions.
May
Jonathan P
JP
Department of Chemistry, The University of British Columbia, Vancouver, B.C., V6T-1Z1 Canada.
Ting
Richard
R
Lermer
Leonard
L
Thomas
Jason M
JM
Roupioz
Yoann
Y
Perrin
David M
DM
D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis; D002413:Cations, Divalent / Q000737:chemistry / Q000378:metabolism; D021881:DNA, Catalytic / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*; D018076:DNA, Complementary / Q000378:metabolism; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000737:chemistry* / Q000378:metabolism*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D012545:Schiff Bases / Q000737:chemistry / Q000378:metabolism
D002413:Cations, Divalent; D021881:DNA, Catalytic; D018076:DNA, Complementary; D012545:Schiff Bases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase