title: Photomodulation of PS-modified oligonucleotides containing azobenzene substituent at pre-selected positions in phosphate backbone.
abstract: A new protocol has been developed for incorporation of a photoisomerizable azobenzene moiety into synthetic stereo-enriched [R(p)] and [S(p)] PS-oligonucleotides. The azobenzene pendant is attached at pre-selected positions in internucleotidic phosphorothioate oligonucleotides of both [R(p)] and [S(p)] diastereomers using a novel reagent, N-iodoacetyl-p-aminoazobenzene, 1. The modified oligomers are purified on HPLC, characterized by LC-MS, and examined for their thermal and photoisomerization properties. The azobenzene moiety imparts greater stability to oligomer duplexes in (E) NN configuration as compared to (Z) configuration. The placement of the azobenzene pendant close to 5'-terminus (n-1) and 3'-terminus of the modified PS-oligos contributes maximum stability to the duplex while a gradual decline in stability occurs with azobenzene moving toward middle of the duplex. Circular Dichroism studies reveal that the chiral environment at the phosphorus center of the PS-oligos does not alter the global conformation of the DNA duplex as such, suggesting conservation of conformation of the modified DNA strands.
authors.affiliation: Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India.
authors.forename: Satyakam
authors.initials: S
authors.lastname: Patnaik
authors.forename: P
authors.initials: P
authors.lastname: Kumar
authors.forename: B S
authors.initials: BS
authors.lastname: Garg
authors.forename: R P
authors.initials: RP
authors.lastname: Gandhi
authors.forename: K C
authors.initials: KC
authors.lastname: Gupta
mesh_terms: D001391:Azo Compounds / Q000737:chemistry*; D002942:Circular Dichroism; D015394:Molecular Structure; D010710:Phosphates / Q000737:chemistry*; D054735:Phosphorothioate Oligonucleotides / Q000737:chemistry*; D010777:Photochemistry; D013237:Stereoisomerism; D013816:Thermodynamics; D010128:p-Aminoazobenzene / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: D001391:Azo Compounds; C526509:N-iodoacetyl-p-aminoazobenzene; D010710:Phosphates; D054735:Phosphorothioate Oligonucleotides; D010128:p-Aminoazobenzene; C009850:azobenzene