Empirical computation of IR and VCD spectra of RNA and spectroscopic analysis of the Tat-TAR interaction.
Item
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Title
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Empirical computation of IR and VCD spectra of RNA and spectroscopic analysis of the Tat-TAR interaction.
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Identifier
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AAI9630521
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identifier
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9630521
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Creator
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Xiang, Ting.
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Contributor
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Adviser: Dixie J. Goss
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Date
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1996
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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, Physical | Chemistry, Biochemistry | Physics, Optics
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Abstract
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In the first part of this thesis, we present models of VCD and IR intensities computation which are based on the exciton approach. The models include degenerate extended coupled oscillator model (DECO), nondegenerate extended oscillator model (NECO) and pseudo-single strand approach (PSS). We also show the necessity to include vibrations other than the C=O stretching motion and improve our computation by adjusting the direction of dipole derivative with respect to the C=O bond direction. We report observed and computed IR and VCD spectra of a number of polyribonucleic acids in D{dollar}\sb2{dollar}O/buffer solution in the 1600-1750 cm{dollar}\sp{lcub}-1{rcub}{dollar} spectral region. The experimental data are compared with results calculated using different levels of sophistication within the exciton approach.;In the second part of this thesis, presented the CD, VCD, stopped-flow and molecular modeling results of a short peptide, which contains the basic region of the HIV-1 Tat (Trans-activator) protein, interacting with {dollar}\Delta{dollar}TAR, a shortened form of native TAR (Trans-activation response element) which is located at the 5{dollar}\sp\prime{dollar} end of the HIV long terminal repeat. The results confirm the conformational changes of both molecules upon binding to each other. Measured and computed VCD spectra suggest a left handed helix structure for the peptide. Kinetic studies indicate a two step mechanism for the binding reaction of these two molecules with k{dollar}\sb1=0.7\times10\sp8\ {lcub}\rm M{rcub}\sp{lcub}-1{rcub}{lcub}\rm sec{rcub}\sp{lcub}-1{rcub}{dollar} and {dollar}\rm k\sb2=69.4\ sec\sp{lcub}-1{rcub}.{dollar}.
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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.
