DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versat...

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Bibliographic Details
Published in:Biomicrofluidics 2014-09, Vol.8 (5), p.052102-052102
Main Authors: Sriram, K K, Chang, Chun-Ling, Rajesh Kumar, U, Chou, Chia-Fu
Format: Article
Language:English
Subjects:
Atomic force microscopy
Condensation polymerization
Deoxyribonucleic acid
DNA
Fluorescence
High pressure oxygen
Immobilization
Microfluidics
Microscopy
Oxygen plasma
Plasma
Polysilsesquioxanes
Ribonucleic acid
RNA
RNA polymerase
SPECIAL TOPIC: SELECTED PAPERS FROM THE ADVANCES IN MICROFLUIDICS AND NANOFLUIDICS 2014 CONFERENCE IN HONOR OF PROFESSOR HSUEH-CHIA CHANG'S 60TH BIRTHDAY
Substrates
Surface roughness
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Summary:Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging.
ISSN:1932-1058
1932-1058
DOI:10.1063/1.4892515