physicochemical fundamentals of dna hybridizations on surfaces

as applied to microarrays and bead-based sequencing technologies


international workshop

Ploen, Germany, May 9 – 12, 2011






Dr. Alexander Pozhitkov, Max-Planck Institute for Evolutionary Biology, Germany

Prof. Peter A. Noble, Alabama State University, USA

Prof. Hans Binder, University of Leipzig, Germany






Many fields of biological science depend upon accurate identification and quantification of nucleic acid targets because these targets indirectly reflect the state of a biological system.  Oligonucleotide microarrays were once thought to be the big hope for the high-throughput identification and quantification of nucleic acids.  At that time, it was believed that designing probes for microarrays and interpreting results was mostly a bioinformatics/statistical exercise.  However, it turned out, that interpreting the signal from microarrays was a major challenge in terms of surface chemistry because many details, such as the interactions between nucleic acid targets in solution and oligonucleotide probes on a microarray surface, were not well understood.  We consider microarray technology as an instrument for measuring concentrations in multicomponent mixtures of DNA or RNA species.  From this point of view, selectivity, response function and reproducibility must be known for appropriate analytics in real world applications.  Other laboratories devised ad hoc approaches to make biological sense of microarray signals.  These approaches have been extensively implemented and are now widely accepted in the published literature.   Recent significant advancements in the understanding of nucleic acid hybridization and dissociation on microarray surfaces have revealed a number of inconsistencies between physical chemistry and the ad hoc approaches.  The purpose of this workshop is three-fold: (i) to update developments in the understanding and application of microarrays, (ii) to identify and resolve inconsistencies in microarray analytics, and (iii) to discuss the future of microarray technology from the perspective of measuring principles and potential applications.  We believe that this workshop is essential for moving forward microarray research and also for the advancement of new technologies such as ‘next-generation’ sequencing, which depend upon surface-hybridizations and array capture.


1.      Recognize contradictions in the theoretical foundation of hybridization-based technologies.

2.      Identify gaps in factual experimental basis of the existing theories.

3.      Suggest future experiments to fill up the gaps.


Group photo

Name, address




Dr. Binder, H.

University of Leipzig, Germany

hook-calibration, Affymetrix, nonspecific hybridization, mismatch, SNP detection, sequence effects

4, 5, 6, 7, 8, 9, 10,  12, 18


Dr. Buhot, A.

Institut Nanoscience et Cryogénie, France

hybridization isotherms, brush effects, thermodynamics, surface effects, spacers

21, 22, 27, 28, 29, 30, 31


Dr. Burden, C.

The Australian National University, Australia

Langmuir models, analysis of spiked-in experiments, physic-chemistry of hybridization, statistics

11, 12, 13, 14


Dr. Carlon, E.

Katolieke Universiteit Leuven, Belgium.

labeling, binding, thermodynamics, Affymetrix, mismatches, nearest neighbor, background subtraction, inverse Langmuir

15, 16, 20, 19,  35, 36, 37, 38, 46, 47, 58, 93


Dr. Gibas, C

Department of Bioinformatics and Genomics UNC – Charlotte

hybridization modeling, background correction

23, 24, 75


Dr. Gamble, L

University of Washigton

surface chemistry, direct probing of surface tethered DNA

17, 49, 50, 79


Dr. Halperin, A.

Université Joseph Fourier, France.

hybridization isotherms, brush effects, thermodynamics, surface effects

27, 28, 29, 30, 31, 32


Dr. Harrison, A.P.

University of Essex, UK

image processing, calibration, Affymetrix, probes, chimeric transcripts, probe sets, outliers

1, 2, 33, 34, 48, 55, 76, 78, 80,  83, 86, 87


Dr. Hooyberghs, J.

VITO, Belgium

thermodynamic equilibrium, nearest neighbor model

37, 38


Dr. Kreil, D.

Boku University Vienna,

University of Cambridge

gene expression profiling, low-level data modelling, idenfication and removal of measurement artefacts, thermodynamic modelling for probe design and signal read-out, signal extraction and normalization

3, 42, 44, 45, 51, 57


Dr. Levicky, R.

New York University, USA

surface hybridization, complementary metal oxide semiconductor

25, 26, 40, 41,  43, 52, 53, 81,  82, 84, 85


Dr. Ott, A.

Universität des Saarlandes, Germany

surface hybridization, hybridization affinity, mismatches and base bulges

56, 59, 60, 61, 62


Dr. Pettitt, B.M.

University of Houston, USA.

surface effects, melting, surface electrostatic effects

39, 74, 90, 91,  92


Dr. Pozhitkov, A.E.

Max-Planck Institute for Evolutionary Biology, Germany

Dr. Noble, P.A.

Alabama State University, USA.

competitive hybridization model, gel-pad oligonucleotide microarrays, probe design, oligonucleotide probes behavior, variability in melting, nonequilibrium thermal dissociation, stringent washing, quantification of multiple nucleic acid targets, nonspecific hybridization, hybridization isotherms, scanner calibration, nearest neighbor

54, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72,  73, 77, 88, 89


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