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BioMEMS and Biomedical Nanotechnology pp 477–496Cite as

Sequence Matters: The Influence of Basepair Sequence on DNA-protein Interactions

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Abstract

The sequencing of the human genome, along with the 200-odd other genomes that have been sequenced, does not represent the solution to a puzzle but rather the necessary introduction to a bigger puzzle. That puzzle is how all the 30,000-odd some genes in the human genome are expressed and controlled in a proper sequence for a cell to function. We can hardly address this enormous problem in this brief review, but instead wish to concentrate on one very small but very important aspect of this problem: physical aspects to how proteins are able to achieve base-pair specific recognition. By “physical aspects” we mean that the proteins distort (strain) the DNA helix when they bind, and if this strain is a function of the sequence of the distorted region then the basepair dependent free energy associated with the strain provides a way to discriminate amongst the basepairs.

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Author information

Authors and Affiliations

  1. Dept. of Physics, Princeton University, Princeton, NJ, 08544, USA

    Yan Mei Wang, Shirley S. Chan & Robert H. Austin

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  1. Yan Mei Wang
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  2. Shirley S. Chan
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  3. Robert H. Austin
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Editor information

Editors and Affiliations

  1. Department of Biomedical Engineering, University of Texas Health Science Center, Houston, TX

    Mauro Ferrari Ph.D. (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President) (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President)

  2. Anderson Cancer Center, University of Texas M.D., Houston, TX

    Mauro Ferrari Ph.D. (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President) (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President)

  3. Rice University, Houston, TX

    Mauro Ferrari Ph.D. (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President) (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President)

  4. University of Texas Medical Branch, Galveston, TX

    Mauro Ferrari Ph.D. (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President) (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President)

  5. Texas Alliance for NanoHealth, Houston, TX

    Mauro Ferrari Ph.D. (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President) (Editor-in-Chief, Professor, Brown Institute of Molecular Medicine Chairman, Professor of Experimental Therapeutics, Professor of Bioengineering, Professor of Biochemistry and Molecular Biology, President)

  6. Dept. of Electrical Engineering, University of California Riverside, Riverside, California, USA

    Mihrimah Ozkan

  7. Dept. of Bioengineering, University of California, San Diego La Jolla, California, USA

    Michael J. Heller

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Wang, Y.M., Chan, S.S., Austin, R.H. (2006). Sequence Matters: The Influence of Basepair Sequence on DNA-protein Interactions. In: Ferrari, M., Ozkan, M., Heller, M.J. (eds) BioMEMS and Biomedical Nanotechnology. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-25843-0_16

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  • DOI: https://doi.org/10.1007/978-0-387-25843-0_16

  • Publisher Name: Springer, Boston, MA

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