TY - JOUR
T1 - Thermodynamic and structural properties of the specific binding between Ag+ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair
AU - Torigoe, Hidetaka
AU - Okamoto, Itaru
AU - Dairaku, Takenori
AU - Tanaka, Yoshiyuki
AU - Ono, Akira
AU - Kozasa, Tetsuo
N1 - Funding Information:
We are grateful to Ms. A. Takamori for her technical assistance in the initial stage of this study. This work was partly supported by the Casio Science Promotion Foundation ; Iketani Science and Technology Foundation ; Nakatani Foundation of Electronic Measuring Technology Advancement ; and Tateishi Science and Technology Foundation . This work was also supported in part by Grant-in-Aid for JSPS Fellows ( 08J07706 to T.K.) from the Ministry of Education, Science, Sports, and Culture of Japan .
PY - 2012/11
Y1 - 2012/11
N2 - Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag + ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag+ ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag + ion. Isothermal titration calorimetry demonstrated that the Ag + ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 106 M-1, which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag+ ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag+ ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences.
AB - Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag + ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag+ ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag + ion. Isothermal titration calorimetry demonstrated that the Ag + ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 106 M-1, which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag+ ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag+ ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences.
KW - Ag ion
KW - C:C mismatched base pair
KW - Large binding affinity
KW - Metal ion-DNA interaction
KW - Metal-mediated base pair
KW - Specific binding
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U2 - 10.1016/j.biochi.2012.06.024
DO - 10.1016/j.biochi.2012.06.024
M3 - Article
C2 - 22766014
AN - SCOPUS:84867395359
VL - 94
SP - 2431
EP - 2440
JO - Biochimie
JF - Biochimie
SN - 0300-9084
IS - 11
ER -