title: Predicting DNA duplex stability on oligonucleotide arrays.
abstract: DNA duplex stability on oligonucleotide microarray was calculated using recently developed electrostatic theory of on-array hybridization thermodynamics. In this method, the first step is to finding the enthalpy and entropy of duplex formation in solution. This standard calculation was done with nearest-neighbor scheme and on-line software. Next the defined parameters and the array's single characteristic, the surface density of probes, are used to predict on-array duplex melting behavior. Reasonable accords of calculated and experimental melting curves for in situ synthesized microfluidic array were observed. The proposed method could be useful in microarray design and hybridization optimization. However, lack of melting curve measurements for different microarray platforms makes more experiments desirable to determine the method's accuracy.
authors.affiliation: College of Veterinary Medicine, Auburn University, AL, USA.
authors.forename: Arnold
authors.initials: A
authors.lastname: Vainrub
authors.forename: Norha
authors.initials: N
authors.lastname: Deluge
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Zhang
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Zhou
authors.forename: Xiaolian
authors.initials: X
authors.lastname: Gao
mesh_terms: D004247:DNA / Q000737:chemistry*; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D004247:DNA