Site-selective depurination by a periodate-dependent deoxyribozyme.

Engineering a selective small-molecule substrate binding site into a deoxyribozyme.

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

Our previous efforts have used in vitro selection to identify numerous Zn(2+)-dependent deoxyribozymes that ligate two RNA substrates with reaction at a 2',3'-cyclic phosphate. Each deoxyribozyme creates one of several different RNA linkages, including native 3'-5' and non-native 2'-5' phosphodiester bonds as well as many unnatural linkages. In this report, we describe experiments to reveal des...

Artificial site-selective DNA cutters to manipulate single-stranded DNA

Recent progress regarding the development of artificial site-selective DNA cutters by chemical approaches are reviewed herein, with a special focus on site-selective cutters for single-stranded DNA. We employ a Ce(IV)/EDTA complex to serve as the catalyst, because it efficiently and selectively cuts single-stranded DNA. Using two complementary oligonucleotide additives, a gap structure is forme...

Bifunctional rhodium intercalator conjugates as mismatch-directing DNA alkylating agents.

A conjugate of a DNA mismatch-specific rhodium intercalator, containing the bulky chrysenediimine ligand, and an aniline mustard has been prepared, and targeting of mismatches in DNA by this conjugate has been examined. The preferential alkylation of mismatched over fully matched DNA is found by a mobility shift assay at concentrations where untethered organic mustards show little reaction. The...

Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone.

DNA glycosylase AlkD excises N7-methylguanine (7mG) by a unique but unknown mechanism, in which the damaged nucleotide is positioned away from the protein and the phosphate backbone is distorted. Here, we show by methylphosphonate substitution that a phosphate proximal to the lesion has a significant effect on the rate enhancement of 7mG depurination by the enzyme. Thus, instead of a convention...