Hybridization thermodynamics of NimbleGen microarrays.

ABSTRACT:

Background

While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets.

Results

We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effec

SUBMITTER: Mueckstein U 

PROVIDER: S-EPMC2823707 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature