Secondary structure in the target as a confounding factor in synthetic oligomer microarray design

Ratushna, Vladyslava G.; Weller, Jennifer W.; Gibas, Cynthia J.

Secondary structure in the target as a confounding factor in synthetic oligomer microarray design

dc.contributor.author	Ratushna, Vladyslava G.	en
dc.contributor.author	Weller, Jennifer W.	en
dc.contributor.author	Gibas, Cynthia J.	en
dc.contributor.department	Biological Sciences	en
dc.date.accessioned	2012-08-24T12:20:38Z	en
dc.date.available	2012-08-24T12:20:38Z	en
dc.date.issued	2005-03-08	en
dc.date.updated	2012-08-24T12:20:38Z	en
dc.description.abstract	Background Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybridization by stable secondary structures in the probe binding site. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment. Results Despite the relatively high hybridization temperatures and 1M monovalent salt imposed in the modeling process to approximate hybridization conditions used in the laboratory, we find that parts of the target molecules are likely to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. For example, at 65°C, 28 ± 7% of the average cDNA target sequence is predicted to be inaccessible to hybridization. We also analyzed the specific binding sites of a set of 70mer probes previously designed for Brucella using a freely available oligo design software package. 21 ± 13% of the nucleotides in each probe binding site are within a double-stranded structure in over half of the folds predicted for the cDNA target at 65°C. The intramolecular structures formed are more stable and extensive when an RNA target is modeled rather than cDNA. When random shearing of the target is modeled for fragments of 200, 100 and 50 nt, an overall destabilization of secondary structure is predicted, but shearing does not eliminate secondary structure. Conclusion Secondary structure in the target is pervasive, and a significant fraction of the target is found in double stranded conformations even at high temperature. Stable structure in the target has the potential to interfere with hybridization and should be a factor in interpretation of microarray results, as well as an explicit criterion in array design. Inclusion of this property in an oligonucleotide design procedure would change the definition of an optimal oligonucleotide significantly.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	BMC Genomics. 2005 Mar 08;6(1):31	en
dc.identifier.doi	https://doi.org/10.1186/1471-2164-6-31	en
dc.identifier.uri	http://hdl.handle.net/10919/18972	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Vladyslava G Ratushna et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Secondary structure in the target as a confounding factor in synthetic oligomer microarray design	en
dc.title.serial	BMC Genomics	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en