DNA structure and environment: Crystallographic studies of monovalent cation-Z-DNA interactions and of an AHMA-DNA complex.
Item
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Title
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DNA structure and environment: Crystallographic studies of monovalent cation-Z-DNA interactions and of an AHMA-DNA complex.
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Identifier
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AAI9908308
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identifier
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9908308
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Creator
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Dong, Xiangchao.
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Contributor
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Adviser: Gary Joseph Quigley
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Date
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1998
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Language
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English
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Publisher
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City University of New York.
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Subject
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Chemistry, Analytical
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Abstract
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DNA, the molecule of heredity, is the basic element in the replication process. Environment (for instance: counterions, water, drug molecules) can affect the structure and the function of DNA. The relations between the structural changes of the DNA molecules under different conditions and the function of the DNA are important research subjects in life science.;Interactions between rubidium, a monovalent cation, and Z-DNA have been studied using X-ray crystallography. Crystals of an oligonucleotide with the sequence of CGCGCG were crystallized with Rb{dollar}\sp+{dollar} as counterion. Data to 1.76 A resolution has been collected under cryogenic condition, to reduce the disorder of the ions in the structure. A total of sixteen rubidium ions have been located with thirteen of them having partial occupancy. The final R value is 17.5%. The result shows that in the Z-DNA, the structures of most monovalent counterions are dynamic--the atoms having fast exchange with water molecules in the crystal.;K-Z-DNA crystals were also obtained from crystallization of an oligonucleotide with the sequence of CGCGCG and with K{dollar}\sp+{dollar} as a counterion. Data was collected using an X-ray diffractometer. Molecular dynamic optimization for the disordered K{dollar}\sp+{dollar} ions in the K-Z-DNA crystal structure was attempted. The K{dollar}\sp+{dollar} position was not reproducible in simulation runs with different conditions. This result indicates that either the method we used is not suitable for solvent disorder calculation or that the ions and solvent are highly disordered that the simulation must involve so many superpositions that it is impossible to distinguish true simulation from noise fitting.;Crystals of an AHMA (3-(9-acridinylamino)-5-(hydroxymethyl) aniline)--d(CGTACG) complex have been obtained after an intensive crystallization condition search. Data with resolution of 2.9 A has been collected using an area detector. The unit cell was found to be a = b = 57.52 A and c = 122.17 A with space group class p321. Attempts have been made to make a heavy metal derivative of the AHMA-DNA complex. Crystals obtained by soaking the AHMA-DNA complex crystal with Sm{dollar}\sp{lcub}3+{rcub}{dollar} showed a unit cell of a = b = 28.54 A and c = 118.41 A with the same space group as the native crystal. Patterson maps for both crystals suggested that the possible base stacking is in the xy plane. Further work has to be done to solve the structure.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
