Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies

• Published in: Nucleic acids research Vol. 33; no. 6; pp. 1767 - 1778
• Main Authors: Narukulla, Raman, Shuker, David E. G., Xu, Yao-Zhong
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-01-2005; Oxford Publishing Limited (England)
• Subjects: 2,4-Dinitrophenol - analogs & derivatives; 2,4-Dinitrophenol - chemical synthesis; 2,4-Dinitrophenol - chemistry; DNA - chemistry; Hypoxanthine - chemistry; Hypoxanthines - chemistry; Inosine - analogs & derivatives; Inosine - chemical synthesis; Inosine - chemistry; Nitrogen - chemistry; Nucleosides - chemistry; Oligodeoxyribonucleotides - chemical synthesis; Oligodeoxyribonucleotides - chemistry; Oligodeoxyribonucleotides - isolation & purification
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gki315

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-β-hydroxyalkyl-hypoxanthines and the availability of the rare base-modified oligomers should offer novel tools for biological and structural studies.