Sensitive Quantitative Nucleic Acid Detection Using Oligonucleotide Microarrays

• Published in: Journal of the American Chemical Society 2003-07, Vol.125 (26), p.7798-7799
• Main Authors: Vainrub, Arnold, Pettitt, B. Montgomery
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Molecular and cellular biology; Nucleic Acids - analysis; Nucleic Acids - chemistry; Oligonucleotide Array Sequence Analysis - methods; RNA, Messenger - analysis; RNA, Messenger - chemistry; Sensitivity and Specificity; Static Electricity; Thermodynamics
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja035020q

We report a new theoretical approach to optimize the performance and quantify the results of gene expression oligonucleotide microarrays which are widely used in biomedical research. An on-array hybridization isotherm that takes into account the screened Coulomb repulsion between the assayed nucleic acid target and the layer of surface tethered oligonucleotide probes is presented. The hybridization efficiency is found as a function of the genomic target (sequence, length, and concentration), array parameters (probe sequence and length, surface probe density), and hybridization conditions (temperature and buffer ionic strength). We present simple relations for the hybridization signal maximum and the linear dynamic detection range and show explicit criteria for optimization. The approach is based on an extension of our recently published theory (Vainrub, A.; Pettitt, B. M. Phys. Rev. E 2002, 66, art. no.-041905) which we generalize here for the cases of target depletion effects and arbitrary target length.