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Quantitative Analysis of Location‐ and Sequence‐Dependent Deamination by APOBEC3G Using Real‐Time NMR Spectroscopy
Author(s) -
Furukawa Ayako,
Sugase Kenji,
Morishita Ryo,
Nagata Takashi,
Kodaki Tsutomu,
TakaoriKondo Akifumi,
Ryo Akihide,
Katahira Masato
Publication year - 2014
Publication title -
angewandte chemie international edition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.831
H-Index - 550
eISSN - 1521-3773
pISSN - 1433-7851
DOI - 10.1002/anie.201309940
Subject(s) - deamination , nuclear magnetic resonance spectroscopy , spectroscopy , sequence (biology) , chemistry , analytical chemistry (journal) , physics , stereochemistry , biochemistry , chromatography , enzyme , quantum mechanics
The human antiretroviral factor APOBEC3G (A3G) deaminates the newly synthesized minus strand of the human immunodeficiency virus 1 (HIV‐1), which results in the abolition of the infectivity of virus‐infectivity‐factor (Vif)‐deficient HIV‐1 strains.1–6 A unique property of A3G is that it deaminates a CCC hot spot that is located close to the 5′ end more effectively than one that is less close to the 5′ end. However, the mechanism of this process is elusive as it includes nonspecific binding of A3G to DNA and sliding of A3G along the DNA strand. Therefore, this process cannot be analyzed by existing methods using the Michaelis–Menten theory. A new real‐time NMR method has been developed to examine the nonspecific binding and the sliding processes explicitly, and it was applied to the analysis of the deamination by A3G. As a result, the location‐dependent deamination can be explained by a difference in the catalytic rates that depend on the direction of the approach of A3G to the target cytidine. Real‐time NMR experiments also showed that A3G deaminates CCCC tandem hotspots with little redundancy, which suggests that A3G efficiently mutates many CCC hotspots that are scattered throughout the HIV‐1 genome.