Position dependent mismatch discrimination on DNA microarrays – experiments and model

Thomas Naiser,Jona Kayser,Timo Mai,Albrecht Ott,Wolfgang Michel

doi:10.1186/1471-2105-9-509

Thomas Naiser, Jona Kayser + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-9-509

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Journal: BMC Bioinformatics	Publication Date: Dec 1, 2008
Citations: 78	License type: CC BY 2.0

Affiliation: University of Bayreuth, Saarland University

Abstract

BackgroundThe propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.ResultsWe observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.ConclusionMolecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.

Highlights

The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR
Position Dependent Influence of Single Base MMs and Bulges on Probe-Target Binding Affinity From the fluorescence micrograph (Fig. 1), we obtain the hybridization signals, which we plot as a function of defect position (Fig. 2)
We observe that the magnitude of mismatch discrimination at a particular defect position depends on the duplex sequence

Summary

Introduction

The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. The well-known double-helix structure of nucleic acids results from sequence-specific binding between complementary single strands. Sequential base pairing between A·T and C·G base pairs along the two complementary strands results in the formation of stable duplexes. This so called hybridization process is fundamental to many biological processes and biotechnologies. Hybridization occurs with single mismatched (MM) base pairs, these duplexes are significantly less stable than the corresponding perfect match (PM) [1, 2]. The single base pair mismatch-discrimination capability of short (~20 nt) oligonucleotide probes provides an important diagnostic (page number not for citation purposes)

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