title: Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies.
abstract: Site-specific modification of the N1-position of purine was explored at the nucleoside and oligomer levels. 2'-deoxyinosine was converted into an N1-2,4-dinitrophenyl derivative 2 that was readily transformed to the desired N1-substituted 2'-deoxyinosine analogues. This approach was used to develop a post-synthetic method for the modification of the endocyclic N1-position of purine at the oligomer level. The phosphoramidite monomer of N1-(2,4-dinitrophenyl)-2'-deoxyinosine 9 was prepared from 2'-deoxyinosine in four steps and incorporated into oligomers using an automated DNA synthesizer. The modified base, N1-(2,4-dinitrophenyl)-hypoxanthine, in synthesized oligomers, upon treatment with respective agents, was converted into corresponding N1-substituted hypoxanthines, including N1-15N-hypoxanthine, N1-methylhypoxanthine and N1-(2-aminoethyl)-hypoxanthine. These modified oligomers can be easily separated and high purity oligomers obtained. Melting curve studies show the oligomer containing N1-methylhypoxanthine or N1-(2-aminoethyl)-hypoxanthine has a reduced thermostability with no particular pairing preference to either cytosine or thymine. The developed method could be adapted for the preparation of oligomers containing mutagenic N1-beta-hydroxyalkyl-hypoxanthines and the availability of the rare base-modified oligomers should offer novel tools for biological and structural studies.
authors.affiliation: Department of Chemistry, The Open University Walton Hall, Milton Keynes, MK7 6AA, UK.
authors.forename: Raman
authors.initials: R
authors.lastname: Narukulla
authors.forename: David E G
authors.initials: DE
authors.lastname: Shuker
authors.forename: Yao-Zhong
authors.initials: YZ
authors.lastname: Xu
mesh_terms: D019297:2,4-Dinitrophenol / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D019271:Hypoxanthine / Q000737:chemistry*; D007042:Hypoxanthines / Q000737:chemistry; D007288:Inosine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry*; D009584:Nitrogen / Q000737:chemistry; D009705:Nucleosides / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry / Q000302:isolation & purification
chemical_list: D007042:Hypoxanthines; C499110:N(1)-(2,4-dinitrophenyl)-2'-deoxyinosine; C499111:N(1)-(2,4-dinitrophenyl)-2'-deoxyinosine phosphoramidite; C499112:N(1)-(2,4-dinitrophenyl)hypoxanthine; D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; D019271:Hypoxanthine; D007288:Inosine; D004247:DNA; D009584:Nitrogen; D019297:2,4-Dinitrophenol