Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution

The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a dire...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2010-04, Vol.114 (14), p.4783-4788
Main Authors: Jin, Kyeong Sik, Shin, Su Ryon, Ahn, Byungcheol, Jin, Sangwoo, Rho, Yecheol, Kim, Heesoo, Kim, Seon Jeong, Ree, Moonhor
Format: Article
Language:English
Subjects:
Circular Dichroism
DNA - chemistry
DNA - drug effects
DNA, Complementary - chemistry
DNA, Complementary - metabolism
Fullerenes - pharmacology
Models, Molecular
Nucleic Acid Conformation - drug effects
Scattering, Small Angle
Solutions
Thermodynamics
X-Ray Diffraction
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Summary:The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.
ISSN:1520-5207
DOI:10.1021/jp9122453