Silver-Stabilized Guanine Duplex: Structural and Optical Properties

被引:14
作者
Chen, Xi [1 ]
Makkonen, Esko [1 ]
Golze, Dorothea [1 ,2 ]
Lopez-Acevedo, Olga [3 ]
机构
[1] Aalto Univ, Dept Appl Phys, Otakaari 1, FI-02150 Espoo, Finland
[2] Aalto Univ, Dept Elect Engn & Automat, POB 13500, Aalto 00076, Finland
[3] Univ Antioquia UdeA, Inst Fis, Grp Fis Atom & Mol, Fac Ciencias Exactas & Nat, Calle 70 52-21, Medellin 050010, Colombia
来源
JOURNAL OF PHYSICAL CHEMISTRY LETTERS | 2018年 / 9卷 / 16期
基金
瑞士国家科学基金会; 芬兰科学院;
关键词
CIRCULAR-DICHROISM; DNA; CLUSTERS; PSEUDOPOTENTIALS; TRANSITION; PAIRS;
D O I
10.1021/acs.jpclett.8b01908
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag+- mediated guanine duplex with two nucleobases per strand, G(2)-Ag-2(+)-G(2). We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G(2)-Ag-2(+)-G(2) is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.
引用
收藏
页码:4789 / 4794
页数:11
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