The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.

ABSTRACT: Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching (PM) complementary sequence a

SUBMITTER: Hooyberghs J 

PROVIDER: S-EPMC2673445 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature