DSSR-PyMOL cartoon-block schematics: PDB entry 1qxb

PDB-id

1qxb; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

NMR structure determination of the self complementary DNA dodecamer cgcgaatt*cgcg in which a ribose is inserted between the 3'-oh of t8 and the 5'-phosphate group of c9

Reference

Nauwelaerts K, Vastmans K, Froeyen M, Kempeneers V, Rozenski J, Rosemeyer H, Van Aerschot A, Busson R, Lacey JC, Efimtseva E, Mikhailov S, Lescrinier E, Herdewijn P (2003): "Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside." Nucleic Acids Res., 31, 6758-6769. doi: 10.1093/nar/gkg911.

Abstract

A ribose residue inserted between the 3'-OH of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information.