Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

Huan H Cao; Nako Nakatsuka; Andrew C Serino; Wei-Ssu Liao; Sarawut Cheunkar; Hongyan Yang; Paul S Weiss; Anne M Andrews

doi:10.1021/acsnano.5b05546

Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

ACS Nano. 2015 Nov 24;9(11):11439-54. doi: 10.1021/acsnano.5b05546. Epub 2015 Oct 6.

Authors

Huan H Cao^{1

2}, Nako Nakatsuka^{1

2}, Andrew C Serino^{1

2

3}, Wei-Ssu Liao^{1

2}, Sarawut Cheunkar^{1

2}, Hongyan Yang⁴, Paul S Weiss^{1

2

3}, Anne M Andrews^{1

2

4}

Affiliations

¹ California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States.
² Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States.
³ Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States.
⁴ Department of Psychiatry and Biobehavioral Health, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles , Los Angeles, California 90095, United States.

PMID: 26426585
DOI: 10.1021/acsnano.5b05546

Abstract

Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.

Keywords: DNA hybridization; alkanethiol patterning; chemical lift-off lithography; nucleotide arrays; self-assembled monolayers.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA / chemistry*
Dimethylpolysiloxanes / chemistry
Microscopy, Atomic Force
Nucleic Acid Hybridization
Photoelectron Spectroscopy
Polyethylene Glycols / chemistry
Printing / methods*
Sulfhydryl Compounds / chemistry

Substances

Dimethylpolysiloxanes
Sulfhydryl Compounds
Polyethylene Glycols
DNA