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Theoretical Study on the Interactions of Metal Ions with DNA Base Pairs

Author: ZhangYu
Tutor: HuangKaiXun
School: Huazhong University of Science and Technology
Course: Inorganic Chemistry
Keywords: Density functional theory Theory of atoms in molecules (AIM) Natural bond orbital (NBO) theory Mφller-Plesset perturbation theory Electrostatic potential Metal ion DNA Tyrosine nitration
CLC: Q75
Type: PhD thesis
Year: 2008
Downloads: 368
Quote: 1
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Abstract


The nucleic acid is one of the most important biological macromolecules, is a carrier of biological information storage and transmission. Metal ions not only in the nucleic acid of biological synthesis, conformational maintain functioning regulation plays an important role, and metals and their complexes with nucleic acid interactions, or the development of anti-cancer drug, the manufacture of the spectroscopic probe and the reactive probe, as well as the basis for the development of DNA-based metal nano-device technology. Thus, it has become one of the topics at the forefront of the study of nucleic acid-depth study of the chemical nature of the metal and nucleic acid interactions. DNA, using high-level quantum chemistry calculation program combined with chemical theory basics, some experimental phenomena and problems that exist on the interaction of metal ions with DNA bases theoretical research, and discussion of this interaction in the meaning of life phenomena: 1 from different metal ions of (Mg 2 Mn 2 . Ni 2 , Zn 2 ) starting in GC Watson-Crick base pair and GG r-Hoogsteen base pairs in the guanine base metal ions into key sites N7 bond by density functional theory, advanced electronic method as well as the AIM and NBO analysis method, a more in-depth to explore the root cause of the presence of metal ions under the double helix of DNA melting temperature Tm differences. From the role of metal ions around the base of the structure, topology analysis and charge distribution, interaction energy and base-pair differences of intermolecular hydrogen bonds, bases of different metal ions before and after the formation of base ions of different energy, different metal ions A comparative study of the compensation of the energy required by the coordination number of changes in the base skeleton changes after different aspects, the results show that the decision to different metal ions under the double helix DNA melting temperature Tm difference is mainly due to different metal ions in the base skeleton changes the coordination number of changes caused by the energy required for compensation due to a difference. 2. Using the density functional theory method, the advanced electronic method as well as the AIM and NBO analysis method, compare different metal ions (Na the Mg 2 and Zn 2 ) in the DNA AT Watson-Crick nucleotide bases metal optimal bit point N7 to the major groove, and the small ditch metal optimal bit node N3 position after coordination geometry, the charge distribution and nucleotide intermolecular hydrogen bonding energy difference discussed the role of different metal sites of the DNA helix structure of bases in the major groove and minor groove hydrogen bonds between bases differences. The results showed that the isolated AT base pairs hydrogen bonds compared hydrated metal ions with the bit with AT base A (N7) bit when hydrogen bonds are significantly different in A (N3). Bit role of AT base pairs A (N3) of the hydrated metal ions can be effectively increased the strength of the base-pair hydrogen bonds between, and thus in the base A at the N3-bit in the position of the minor groove of DNA also may be a potential of the metal anti- cancer drug chemotherapy bonding sites. 3 using the density functional theory method, the advanced electronic method as well as the AIM analysis method, discuss different metal ions from the geometry of the interaction can be the critical point of the charge density as well as the role of net charge on G4 polymer structure stability the impact and G4 polymer metal ion selectivity. Calculated by in B3LYP/SDD and MPWB95/6-31 G (d, p) and MP2/6-31G theoretical calculation level, the metal ion complexes of the G4-MZ-G4 (MZ = Li , Na , K , Rb , Cs , Mg 2 , Ca < sup> 2 Sr 2 , the Ba 2 ), intermolecular interactions can order found that even hydration can be corrected or not, are in contradiction with the experimental results. G4-M -G4 complexes, AIM analysis showed that OM interactions critical point on the size of the charge density ρb order for K gt ; Na gt; Li , which means in the G4-M -G4 complex K than Na and Li to be stable, and the stability of the experimental results K gt; the of Na gt; gt; Li consistent, G4-MZ-G4 complex metal ion selectivity depends on the \4 using theoretical methods B3LYP/6-31 G (d, p), base pairs (GC Watson-Crick base pairs the GG of r-Hoogsteen base pairs and AT Watson-Crick base pairs) in the hydrated metal ions before and after the electrostatic potential changes were calculated. From the electrostatic potential of the base pairs that metal positive ions with bases in multiple sites into a key. Not observed, the basic metal ions in the base pairs of the negative electric potential bit points into key base pairs of the negative potential area, while positive potential area expanded and positive potential value increases. This can be inferred that the metal ions base pair changes before and after its electrostatic potential will inevitably change the micro-environment of the bases around, causing the corresponding structure, dynamics and the changing nature of. 5 B3LYP/6-31 G (d, p) theoretical methods, and AIM theoretical analysis to explore the role of glutamate ions in protein tyrosine nitration (Yz). The presence of glutamate ion the Yz nature, the formation mechanism of glutamate ion Yz · how to guide the · of NO 2 NT to form a near-to-Yz · possible proton transfer mechanism, etc. The aspects of the study. The results show that the YZ the vicinity of the residues Glu ions through it the hydrogen significantly affect the electronic properties of the YZ residues; the same time, Glu ions in the vicinity of YZ residues contribute to the formation of a stable intermediate complexes M1 with YZ residues formed and guide the nitrating agent to reach the YZ ·-OH ortho to C atoms, these effects are mainly dependent on the N 17 ... O 15 interactions (this effect · NO 2 perpendicular to the plane). Glu residues in the presence of a YZ residues near also helps complexes M2 through double proton synergistic migrate to a more stable complexes M3 Glu ion catalyzes the proton migration as a proton switch confirms the experimental results, theoretically , i.e. in the vicinity of Yz negative valence residue is a key determining nitrification loci.

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