title: Charge-neutral morpholino microarrays for nucleic acid analysis.
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.
authors.affiliation: Department of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA.
authors.forename: Wanqiong
authors.initials: W
authors.lastname: Qiao
authors.forename: Sergey
authors.initials: S
authors.lastname: Kalachikov
authors.forename: Yatao
authors.initials: Y
authors.lastname: Liu
authors.forename: Rastislav
authors.initials: R
authors.lastname: Levicky
mesh_terms: D002623:Chemistry Techniques, Analytical / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D015335:Molecular Probes / Q000737:chemistry*; D060172:Morpholinos / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013499:Surface Properties
chemical_list: D015335:Molecular Probes; D060172:Morpholinos; D004247:DNA