Nucleic Acids Research Advance Access published online on June 21, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn370
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Methods Online |
Real-time detection of Fe·EDTA/H2O2-induced DNA cleavage by linear dichroism
1Department of Chemistry, Yeungnam University, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea and 2School of Herb Medicine Resource, Kyungwoon University, Kumi, Gyeong-buk, 730-852, Republic of Korea
*To whom correspondence should be addressed. Tel: +82 53 810 2362; Fax: +82 53 815 5412; Email: seogkim{at}ynu.ac.kr
Received February 13, 2008. Revised April 23, 2008. Accepted May 27, 2008.
The conditions for the measurement of linear dichroism (LD) can be adjusted so as to solely reflect the length and the flexibility of DNA. The real-time detection of the EDTA·Fe2+-induced oxidative cleavage of double-stranded native and synthetic DNAs was performed using LD. The decrease in the magnitude of the LD at 260 nm, which reflects an increase in the flexibility and a decrease in the length of the DNA, can be described by the sum of two or three exponential curves in relation to the EDTA·Fe2+ concentration. The fast component was assigned to the cleavage of one of the double strands, inducing an increase in the flexibility, while the other slower component was assigned to the cleavage of the double strand, resulting in the shortening of DNA. The decrease in the magnitude of the LD of poly[d(A-T)2] was similar to that of poly[d(I-C)2], while that of poly[d(G-C)2] was found to be the slowest, indicating that the resistance of poly[d(G-C)2] against the Fenton-type reagent was the strongest. This observation suggests that the amine group in the minor groove of the double helix may play an important role in slowing the EDTA·Fe2+-induced oxidative cleavage.