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Journal of Mechanical Science and Technology

, Volume 33, Issue 11, pp 5311–5319 | Cite as

Effect of non-uniform fields on DNA entering nano-channel

  • Minsub HanEmail author
  • Byoung Choul Kim
Article
  • 13 Downloads

Abstract

The translocation of deoxyribonucleic-acid (DNA) segments into a nanoscale channel from a bulk solution has significance to genome-related fields such as gene sequencing and genetic profiling. However, its dynamic characteristics are poorly understood because of complexities involving the size and character of the confining spaces, polymeric evolution, and driving sources. The DNA translocation was studied by mesoscale simulation using a worm-like-chain model of DNA and the dissipative particle dynamics method. Three driving sources — electric field, suction flow, and constant body force were individually applied to a λ-DNA entering a nanoscale cylindrical channel. Each source altered the translocation actions, mainly due to marked differences in conformational transformation processes. The suction flow uniquely induced strong extension of the DNA chain before channel entry. Consequently, the flow was more effective at overcoming the free-energy barrier with narrower confinements. Other driving sources permitted the DNA chain to enter in a more globular form, which was effective for larger entrances. Combining different sources is the most versatile means of controlling the trans-location of genetic materials in highly confined spaces.

Keywords

Crack Gene sequencing Molecular dynamics simulation Nanochannel 

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Notes

Acknowledgments

This work was supported by the Incheon National University Research Grant in 2015.

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Copyright information

© KSME & Springer 2019

Authors and Affiliations

  1. 1.Department of Mechanical EngineeringIncheon National UniversityIncheonKorea
  2. 2.Division of Nano-BioengineeringIncheon National UniversityIncheonKorea

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