Direct Visualization of DNA Recognition by Restriction Endonuclease EcoRI

Chiung Fang Huang, Pei Wen Peng, Chih Ming Cheng, Jing Shin Tsai, Wei Ting Wang, Chien Ting Hsu, Keng Liang Ou, Tzu Sen Yang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background/Purpose: Restriction endonuclease is found in bacteria and can precisely cut off the DNA sequence specificity invaded from outside. Using the restriction endonuclease to cleave the double-stranded DNA at specific recognition nucleotide sequences is regarded as important biotechnology. However, traditional approaches cannot directly observe the process of specific binding of DNA by the restriction endonuclease. Methods: Single-molecule biotechnologies, including an optical tweezers system and single-molecule fluorescence detection system, were proposed to directly observe how the restriction endonuclease EcoRI found the recognition-binding site. Results: Overall, the study showed that EcoRI conjugated quantum dots (QDs) possessed the ability to recognize its specific binding sites. In addition, the distributions of the QD-EcoRI trajectory in the transverse direction were nearly the same; however, the difference occurred in the longitudinal direction along the DNA axis during the early and late stages of EcoRI recognition. Conclusion: These results suggest one-dimensional sliding of EcoRI existed along the DNA contour during EcoRI recognition. In addition, when EcoRI slided along the DNA contour, it would require more than 400 seconds for EcoRI to correctly find its DNA target site.

Original languageEnglish
Pages (from-to)25-29
Number of pages5
JournalJournal of Experimental and Clinical Medicine(Taiwan)
Volume5
Issue number1
DOIs
Publication statusPublished - 2013

Fingerprint

Deoxyribonuclease EcoRI
DNA Restriction Enzymes
DNA
Quantum Dots
Biotechnology
Binding Sites
Optical Tweezers
Optical Devices
Deoxyribonuclease I
Fluorescence
Bacteria

Keywords

  • Optical tweezers
  • Quantum dots
  • Restriction endonucleases
  • Single-molecule fluorescence detection
  • Single-molecule manipulation

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Direct Visualization of DNA Recognition by Restriction Endonuclease EcoRI. / Huang, Chiung Fang; Peng, Pei Wen; Cheng, Chih Ming; Tsai, Jing Shin; Wang, Wei Ting; Hsu, Chien Ting; Ou, Keng Liang; Yang, Tzu Sen.

In: Journal of Experimental and Clinical Medicine(Taiwan), Vol. 5, No. 1, 2013, p. 25-29.

Research output: Contribution to journalArticle

Huang, Chiung Fang ; Peng, Pei Wen ; Cheng, Chih Ming ; Tsai, Jing Shin ; Wang, Wei Ting ; Hsu, Chien Ting ; Ou, Keng Liang ; Yang, Tzu Sen. / Direct Visualization of DNA Recognition by Restriction Endonuclease EcoRI. In: Journal of Experimental and Clinical Medicine(Taiwan). 2013 ; Vol. 5, No. 1. pp. 25-29.
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