title: An efficient binding chemistry for glass polynucleotide microarrays.
abstract: A variety of methods have been described for making synthetic polynucleotide microarrays. These include in situ synthesis directly on the array surface, for example, by photolithography or ink-jet printing technologies, and the application of presynthesized polynucleotides that are derivatized with various nucleophiles or electrophiles. In the latter case, a variety of surface chemistries have been developed, and several are available commercially. These chemistries must be compatible with nanoliter-scale volumes of polynucleotide reagents, which contact the array over a small portion of their surface. We reasoned that a three-dimensional polymer coating could potentially offer greater surface contact and higher binding efficiency. Here we describe a polyethylenimine-based coating chemistry that provides exceptional binding and hybridization characteristics. In our preferred process, size-fractionated polyethylenimine polymers are cross-linked onto an aminopropylsilanated glass surface in the presence of cyanuric chloride. The resulting three-dimensional coating binds polynucleotides through a mixture of covalent and noncovalent interactions as evidenced by comparisons between 5'-aminoalkyl modified and unmodified polynucleotides. Binding and hybridization comparisons are presented including analogous two-dimensional electrophilic and electrostatic chemistries.
authors.affiliation: Incyte Genomics, Microarray Research and Development, 6519 Dumbarton Circle, Fremont, California 94555, USA.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Lee
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Sawan
authors.forename: Zora
authors.initials: Z
authors.lastname: Modrusan
authors.forename: Lyle J
authors.initials: LJ
authors.lastname: Arnold
authors.forename: Mark A
authors.initials: MA
authors.lastname: Reynolds
mesh_terms: D000465:Algorithms; D003432:Cross-Linking Reagents; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005898:Glass; D017403:In Situ Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011094:Polyethyleneimine / Q000737:chemistry*; D015347:RNA Probes; D012333:RNA, Messenger / Q000096:biosynthesis; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017550:Spectroscopy, Fourier Transform Infrared; D013499:Surface Properties; D014227:Triazines
chemical_list: D003432:Cross-Linking Reagents; D015347:RNA Probes; D012333:RNA, Messenger; D014227:Triazines; C019309:cyanuric chloride; D011094:Polyethyleneimine; D004247:DNA