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The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences, and positional contexts, could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex, and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick to Hoogsteen transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape framework. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of Watson-Crick and Hoogsteen base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a difficult target for both simulation and experiment.
This article was published in the following journal.
Name: The journal of physical chemistry letters
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Electric power supply devices which convert biological energy, such as chemical energy of metabolism or mechanical energy of periodic movements, into electrical energy.
The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.
A set of opposing, nonequilibrium reactions catalyzed by different enzymes which act simultaneously, with at least one of the reactions driven by ATP hydrolysis. The results of the cycle are that ATP energy is depleted, heat is produced and no net substrate-to-product conversion is achieved. Examples of substrate cycling are cycling of gluconeogenesis and glycolysis pathways and cycling of the triglycerides and fatty acid pathways. Rates of substrate cycling may be increased many-fold in association with hypermetabolic states resulting from severe burns, cold exposure, hyperthyroidism, or acute exercise.
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Thermal energy contained in the earth. It can be used directly to supply heat or converted to mechanical or electrical energy. (from McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
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