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Mechanical Properties of DNA
The mechanical properties of DNA (deoxyribonucleic acid) have attracted the interest of both biophysicists and biologists because of the influence of these properties on numerous biological processes, such as DNA transcription, gene expression and regulation, and DNA replication. The elastic properties of the DNA molecule determine how it supercoils during replication, how it packs into confined biological structures and how it interacts with proteins during gene expression.
The recently published Advanced Mechanical Models of DNA Elasticity is devoted to an analysis of more than twenty existing mechanical models of DNA, and the development of more comprehensive models of DNA elasticity. The existing models are based on discrete statistical mechanics, atomistic, continuum, dynamic, and approximation methods. Our analysis of these models shows that they yield some unphysical results specifically for applied forces of less than 10 pN and complicated solutions for large forces (more than 65 pN). To overcome these deficiencies we have developed more comprehensive models including the Explicit Functional Helicoidal Model (EHM) which can describe the stretching of DNA including the transition of dsDNA to S-DNA and molecular overwinding. The results of calculations with this model are in good agreement with experimental data. The model is simpler than other known models that reflect the transition from dsDNA to S-DNA or ssDNA. The EHM model works in a large range of stretching forces and applied torques. Possible coiled ribbon applications for the single stranded ssDNA modeling (EHMR) at strong stretching and corresponding stress evaluation are also studied. We also study the buckling of a DNA molecule and DNA mechanical stability.
As a result, we have found that the EHM is more comprehensive in comparison with other known mechanical models of the DNA, not only in the mathematical representation of the principal static and dynamical features of its elasticity and transitions, but also in the correct description of the molecule’s helical structure and geometric parameters.
In addition, we discuss the experimental techniques for determining the mechanical properties of DNA, including: force application by solution flow, stretching micropipette, glass needles, optical and magnetic tweezers; the measurement of force and displacement by atomic force microscopy (AFM) including high mode vibration with increased sensitivity; and small-angle X-ray scattering interference measurements of molecular length fluctuations. Micromanipulation techniques are also considered, including different types of cantilevers and effective flexure hinges with a variety of profiles.
Advanced Mechanical Models of DNA Elasticity reflects the author’s experience and represents his ideas and opinions. Results of many other researchers in this field are also discussed in the book.
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About the Author
Dr. Yakov Tseytlin is a mechanical engineer, educator, and research scientist. He has contributed numerous articles to professional journals, and authored 4 monographs. He is also a member of the International Society of Automation (recognition awards 1998-2012, ISA). His achievements include development of methods and concepts in micro elasticity, DNA elasticity modeling, atomic force microscopy, and information criterion of measurement uncertainty negligibility.
Biomedicine & Biochemistry
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