Charge-neutral morpholino microarrays for nucleic acid analysis

Wanqiong Qiao, Sergey Kalachikov, Yatao Liu, Rastislav Levicky

Research output: Contribution to journalArticle

Abstract

A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.

Original languageEnglish (US)
Pages (from-to)207-214
Number of pages8
JournalAnalytical Biochemistry
Volume434
Issue number2
DOIs
StatePublished - Mar 15 2013

Fingerprint

Morpholinos
Microarrays
Nucleic Acids
DNA
Osmolar Concentration
Ionic strength
Printing
Nucleic Acid Probes
DNA Probes
Static Electricity
Aldehydes
Surface-Active Agents
Immobilization
Adsorption
Electrostatics
Stabilization
Tuning

Keywords

  • DNA
  • Immobilization
  • Microarrays
  • Morpholinos
  • PNA
  • Surface hybridization

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology
  • Cell Biology

Cite this

Charge-neutral morpholino microarrays for nucleic acid analysis. / Qiao, Wanqiong; Kalachikov, Sergey; Liu, Yatao; Levicky, Rastislav.

In: Analytical Biochemistry, Vol. 434, No. 2, 15.03.2013, p. 207-214.

Research output: Contribution to journalArticle

Qiao, Wanqiong ; Kalachikov, Sergey ; Liu, Yatao ; Levicky, Rastislav. / Charge-neutral morpholino microarrays for nucleic acid analysis. In: Analytical Biochemistry. 2013 ; Vol. 434, No. 2. pp. 207-214.
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