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 complementary sequence and o

ORGANISM(S): synthetic construct

SUBMITTER: Paul Van Hummelen 

PROVIDER: E-GEOD-14547 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress