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Analytical and Bioanalytical Chemistry

, Volume 408, Issue 23, pp 6453–6459 | Cite as

Direct and precise length measurement of single, stretched DNA fragments by dynamic molecular combing and STED nanoscopy

  • Namdoo Kim
  • Hyung Jun Kim
  • Younggyu Kim
  • Kyung Suk Min
  • Seong Keun Kim
Research Paper

Abstract

A combination of DNA stretching method and super-resolution nanoscopy allows an accurate and precise measurement of the length of DNA fragments ranging widely in size from 117 to 23,130 bp. BstEII- and HindIII-treated λDNA fragments were stained with an intercalating dye and then linearly stretched on a coverslip by dynamic molecular combing. The image of individual DNA fragments was obtained by stimulated emission depletion nanoscopy. For DNA fragments longer than ∼1000 bp, the measured lengths of DNA fragments were consistently within ∼0.5 to 1.0 % of the reference values, raising the possibility of this method in a wide range of applications including facile detection for copy number variations and trinucleotide repeat disorder.

Keywords

DNA Dynamic molecular combing Length measurement STED nanoscopy 

Notes

Acknowledgments

We thank Professor Stefan W. Hell of Max Planck Institute for Biophysical Chemistry for the permission to use the Imspector imaging program. This research was supported by the Global Frontier Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (NRF-2014M3A6A4075063). We also acknowledge the BK21 Plus Program and SNU Brain Fusion Grant.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

216_2016_9764_MOESM1_ESM.pdf (369 kb)
ESM 1 (PDF 369 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Namdoo Kim
    • 1
  • Hyung Jun Kim
    • 1
  • Younggyu Kim
    • 1
    • 2
  • Kyung Suk Min
    • 3
  • Seong Keun Kim
    • 1
    • 3
  1. 1.Department of ChemistrySeoul National UniversitySeoulRepublic of Korea
  2. 2.LumiMac, Inc.SeoulKorea
  3. 3.Department of Biophysics and Chemical BiologySeoul National UniversitySeoulRepublic of Korea

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