title: Enhancing the fluorescence intensity of DNA microarrays by using cationic surfactants.
abstract: DNA microarrays have been used as powerful tools in genomics studies and single nucleotide polymorphisms analysis. However, the fluorescence detection used in most conventional DNA microarrays is still limited by its sensitivity. The aim of this study is to use a cationic surfactant, cetyl trimethylammonium bromide (CTAB), to enhance the fluorescence intensity of 6-carboxy-fluorescene (FAM)-labeled DNA probes immobilized on a DNA microarray. We show that in the presence of CTAB the immobilized FAM-labeled DNA probes is 11-fold brighter than that without exposure to CTAB. Similarly, when we hybridize FAM-labeled DNA targets to a DNA microarray and treat the surface with CTAB solution, the fluorescence intensity shows a 26-fold increase for perfect-match DNA targets. More importantly, the contrast between perfect-match and 1-mismatch DNA is also increased from 1.3-fold to 15-fold. This method offers a simple and efficient technique to enhance the detection limit of DNA microarrays.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, Singapore 117576.
authors.forename: Siok Lian
authors.initials: SL
authors.lastname: Lai
authors.forename: Chih-Hsin
authors.initials: CH
authors.lastname: Chen
authors.forename: Kun-Lin
authors.initials: KL
authors.lastname: Yang
mesh_terms: D001483:Base Sequence; D002232:Carbocyanines / Q000737:chemistry; D000077286:Cetrimonium; D002593:Cetrimonium Compounds / Q000737:chemistry; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D005452:Fluoresceins / Q000737:chemistry; D057230:Limit of Detection; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012996:Solutions; D013050:Spectrometry, Fluorescence; D013501:Surface-Active Agents / Q000737:chemistry*
chemical_list: D002232:Carbocyanines; D002593:Cetrimonium Compounds; D015342:DNA Probes; D005452:Fluoresceins; D012996:Solutions; D013501:Surface-Active Agents; C089187:cyanine dye 3; C024098:6-carboxyfluorescein; D000077286:Cetrimonium