title: Assessment of fluorescence resonance energy transfer for two-color DNA microarray platforms.
abstract: Two-color DNA microarray platforms are widely used for determining differential amounts of target sequences in parallel between sample pairs. However, the fluorescence (or Forster) resonance energy transfer (FRET) between two fluorophores can potentially result in the distortions of the measured fluorescence signals. Here we assessed the influence of FRET on the two-color DNA microarray platform and developed a reliable and convenient method for the correction of FRET distortion. Compared to current methods of normalization based on the statistical analysis and the hypothesis that only a small part of target sequences are differentially presented between sample pairs, our FRET correction method can recover the undistorted signals by the compensation of fluorescence emission, without considering the number of target sequences differentially presented. The correction method was validated with samples at different target ratios and with microarrays spotted in different probe concentrations. We also applied the FRET correction method to gene expression profiling arrays, and the results show that FRET was present when the content of target sequence was beyond a threshold amount and that the process incorporating our FRET correction method can improve the reliability of the gene expression profiling microarray platform in comparison with the current process without FRET correction.
authors.affiliation: Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People's Republic of China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Zhu
authors.forename: Ying
authors.initials: Y
authors.lastname: Lu
authors.forename: Cheng
authors.initials: C
authors.lastname: Deng
authors.forename: Guoliang
authors.initials: G
authors.lastname: Huang
authors.forename: Shengyi
authors.initials: S
authors.lastname: Chen
authors.forename: Shukuan
authors.initials: S
authors.lastname: Xu
authors.forename: Yi
authors.initials: Y
authors.lastname: Lv
authors.forename: Keith
authors.initials: K
authors.lastname: Mitchelson
authors.forename: Jing
authors.initials: J
authors.lastname: Cheng
mesh_terms: D002138:Calibration; D004247:DNA / Q000032:analysis*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes; D004247:DNA