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Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array

Lookup NU author(s): Professor Neil Boonham

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

Background: The performance of probes on an oligonucleotide microarray can be characterised in terms of hybridisation signal strength and the ability to discriminate sequence mismatches between the probe and the hybridising target strand, such as those resulting from SNPs. Various properties of the probe affect mismatch discrimination, such as probe length and the position of mismatched bases, and the effects of these factors have been well characterised in a variety of array formats. Results: A low-density microarray was developed to systematically investigate the effect of a probe's position within hybridised target PCR products on the tolerance and discrimination of single-nucleotide mismatches between the probe and target. In line with previous reports, hybridisation signals were attenuated by different degrees depending on the identity of the mismatch, the position of the mismatch within the probe, and the length of the PCR product. However, the same mismatch caused different degrees of attenuation depending on the position of the probe within the hybridising product, such that improved mismatch discrimination was observed for PCR products where a greater proportion of the total length was proximal to the array surface. Conclusions: These results suggest that the degree of mismatch discrimination can be influenced by the choice of PCR primers, providing a means by which array performance could be fine-tuned in addition to manipulation of the properties of the probes themselves. © 2014 Tomlinson et al.; licensee BioMed Central Ltd.


Publication metadata

Author(s): Tomlinson J, Harrison C, Boonham N, Goodchild SA, Weller SA

Publication type: Article

Publication status: Published

Journal: BMC Research Notes

Year: 2014

Volume: 7

Issue: 1

Online publication date: 17/04/2014

Acceptance date: 09/04/2014

ISSN (electronic): 1756-0500

Publisher: BioMed Central Ltd

URL: https://doi.org/10.1186/1756-0500-7-251

DOI: 10.1186/1756-0500-7-251

PubMed id: 24742004


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