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Direct Observation of Single Molecule Conformational Change of Tight-Turn Paperclip DNA Triplex in Solution

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Abstract

DNA triplex modulates gene expression by forming stable conformation in physiological condition. However, it is not feasible to observe this unique molecular structure of large molecule with 54 oligodeoxynucleotides directly by conventional nuclear magnetic approach. In this study, we observed directly single molecular images of paperclip DNA triplexes formation in a buffer solution of pH 6.0 by atomic force microscopy (AFM). Meanwhile, a diffuse “tail” of unwound DNA was observed in pH 8.0 solution. This designable approach in visualizing the overall structures and shapes of oligo-DNAs at the single molecular level, by AFM, is applicable to other biopolymers as well.

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Abbreviations

AFM:

atomic force microscopy

TFOs:

triplex-forming oligodeoxynucleotides

NMR:

nuclear magnetic resonance

CD:

circular dichroism

PITPNM 3:

phosphatidylinositol transfer protein membrane-associated genes

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Acknowledgements

The authors thank for the BioAFM supported by Department of Biological Sciences and Technology at National Chiao Tung University, and National Nano Device Laboratories. The work is supported by National Science Council of Taiwan (NSC 95-2113-M-001-043-MY2 and NSC 97-2112-M-009-MY3 to LSK and CCC, respectively) and Academia Sinica.

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Authors and Affiliations

  1. Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan

    Ching-Ping Liu, Ming-Tsai Wey & Lou-Sing Kan

  2. College of Life Science, National Tsinghua University, Hsinchu, 300, Taiwan

    Ming-Tsai Wey

  3. Department of Biological Sciences and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan

    Chia-Ching Chang

  4. Institute of Physics, Academia Sinica, Taipei, 11529, Taiwan

    Chia-Ching Chang

  5. Department of Bioengineering, Tatung University, Taipei, 104, Taiwan

    Lou-Sing Kan

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  1. Ching-Ping Liu
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  2. Ming-Tsai Wey
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Correspondence to Chia-Ching Chang or Lou-Sing Kan.

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Liu, CP., Wey, MT., Chang, CC. et al. Direct Observation of Single Molecule Conformational Change of Tight-Turn Paperclip DNA Triplex in Solution. Appl Biochem Biotechnol 159, 261–269 (2009). https://doi.org/10.1007/s12010-008-8390-1

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  • DOI: https://doi.org/10.1007/s12010-008-8390-1

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