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Kim SH, Kim H, Jeong H, Yoon TY. Encoding Multiple Virtual Signals in DNA Barcodes with Single-Molecule FRET. NANO LETTERS 2021; 21:1694-1701. [PMID: 33586985 DOI: 10.1021/acs.nanolett.0c04502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
DNA barcoding provides a way to label a myriad of different biological molecules using the extreme programmability in DNA sequence synthesis. Fluorescence imaging is presumably the most easy-to-access method for DNA barcoding, yet large spectral overlaps between fluorescence dyes severely limit the numbers of barcodes that can be detected simultaneously. We here demonstrate the use of single-molecule fluorescence resonance energy transfer (FRET) to encode virtual signals in DNA barcodes using conventional two-color fluorescence microscopy. By optimizing imaging and biochemistry conditions for weak DNA hybridization events, we markedly enhanced accuracy in our determination of the single-molecule FRET efficiency exhibited by each binding event between DNA barcode sequences. This allowed us to unambiguously differentiate six DNA barcodes encoding different FRET values without involving any probe sequence exchanges. Our method can be directly incorporated with previous DNA barcode techniques, and may thus be widely adopted to expand the signal space of DNA barcoding.
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Affiliation(s)
- Sung Hyun Kim
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Hyunwoo Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Hawoong Jeong
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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2
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Nomidis SK, Szymonik M, Venken T, Carlon E, Hooyberghs J. Enhancing the Performance of DNA Surface-Hybridization Biosensors through Target Depletion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12276-12283. [PMID: 31433651 DOI: 10.1021/acs.langmuir.9b01761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large, and they have high affinity for the target, the DNA in solution may become depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration c2) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration c1 ≫ c2). We show that depletion can give rise to a strongly enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations c2/c1 that are up to 3 orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich and exhibits a nonmonotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.
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Affiliation(s)
- Stefanos K Nomidis
- Laboratory for Soft Matter and Biophysics , KU Leuven , Celestijnenlaan 200D , 3001 Leuven , Belgium
- Flemish Institute for Technological Research (VITO) , Boeretang 200 , B-2400 Mol , Belgium
| | - Michal Szymonik
- Flemish Institute for Technological Research (VITO) , Boeretang 200 , B-2400 Mol , Belgium
| | - Tom Venken
- Center for Cancer Biology , VIB , 3000 Leuven , Belgium
- Laboratory of Translational Genetics, Department of Human Genetics , KU Leuven , 3000 Leuven , Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics , KU Leuven , Celestijnenlaan 200D , 3001 Leuven , Belgium
| | - Jef Hooyberghs
- Flemish Institute for Technological Research (VITO) , Boeretang 200 , B-2400 Mol , Belgium
- Theoretical Physics , Hasselt University , Campus Diepenbeek , B-3590 Diepenbeek , Belgium
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de Bruin D, Bossert N, Aartsma-Rus A, Bouwmeester D. Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides. J Nanobiotechnology 2018; 16:37. [PMID: 29622040 PMCID: PMC5887185 DOI: 10.1186/s12951-018-0361-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/21/2018] [Indexed: 01/07/2023] Open
Abstract
Background Short nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson–Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided. Results We employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results. Conclusion The primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data. Electronic supplementary material The online version of this article (10.1186/s12951-018-0361-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donny de Bruin
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.
| | - Nelli Bossert
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands
| | | | - Dirk Bouwmeester
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.,Department of Physics, University of California, Santa Barbara, CA, 93106, USA
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4
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Rivard BR, Cooper CJ, Stubbs JM. The role of differing probe and target strand lengths in DNA microarrays investigated via Monte Carlo molecular simulation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Mohammadi-Kambs M, Hölz K, Somoza MM, Ott A. Hamming Distance as a Concept in DNA Molecular Recognition. ACS OMEGA 2017; 2:1302-1308. [PMID: 28474009 PMCID: PMC5410656 DOI: 10.1021/acsomega.7b00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/17/2017] [Indexed: 06/07/2023]
Abstract
DNA microarrays constitute an in vitro example system of a highly crowded molecular recognition environment. Although they are widely applied in many biological applications, some of the basic mechanisms of the hybridization processes of DNA remain poorly understood. On a microarray, cross-hybridization arises from similarities of sequences that may introduce errors during the transmission of information. Experimentally, we determine an appropriate distance, called minimum Hamming distance, in which the sequences of a set differ. By applying an algorithm based on a graph-theoretical method, we find large orthogonal sets of sequences that are sufficiently different not to exhibit any cross-hybridization. To create such a set, we first derive an analytical solution for the number of sequences that include at least four guanines in a row for a given sequence length and eliminate them from the list of candidate sequences. We experimentally confirm the orthogonality of the largest possible set with a size of 23 for the length of 7. We anticipate our work to be a starting point toward the study of signal propagation in highly competitive environments, besides its obvious application in DNA high throughput experiments.
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Affiliation(s)
- Mina Mohammadi-Kambs
- Biological
Experimental Physics, Saarland University, Campus B2.1, 66123 Saarbrücken, Germany
| | - Kathrin Hölz
- Institute
of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute
of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Albrecht Ott
- Biological
Experimental Physics, Saarland University, Campus B2.1, 66123 Saarbrücken, Germany
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6
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Cabral-Castro MJ, Peralta RHS, Cavalcanti MG, Puccioni-Sohler M, Carvalho VL, da Costa Vasconcelos PF, Peralta JM. A Luminex-based single DNA fragment amplification assay as a practical tool for detecting and serotyping dengue virus. J Virol Methods 2016; 236:18-24. [PMID: 27393681 DOI: 10.1016/j.jviromet.2016.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 06/07/2016] [Accepted: 07/04/2016] [Indexed: 10/21/2022]
Abstract
Dengue is a mosquito-borne viral infection that can evolve from subclinical to severe forms of disease. Early recognition during initial primary and secondary infections correlates with a reduced case-fatality rate in susceptible groups. The aim of this study was to standardize a DNA hybridization assay based on the Luminex technology for detecting and serotyping dengue virus (DENV). Reference DENVs representing the four different serotypes were used as controls to standardize the test. For validation, 16 DENV isolates obtained from a reference laboratory were analyzed in a double-blind manner to validate the test. Sixty blood samples from patients suspected of having dengue fever were used to evaluate the methodology after the validation step, and the results were compared with the reference semi-nested RT-PCR. Additionally, five human samples of each Zika and Chikungunya confirmed patients were used for specificity analysis. The Luminex-based assay correctly identified all 16 DENV isolates. In the evaluation step, the results of the RT-PCR/Luminex assay showed a concordance of 86.7% with those of the semi-nested RT-PCR. None of other virus infection samples was amplified. This is the first description of a hybridization assay that can discriminate the four DENV serotypes using probes against a single DENV sequence. The results indicated that the RT-PCR/Luminex DENV assay designed and evaluated in this study is a valuable additional tool for the early and rapid detection and serotyping of DENV, which could, in the future, be applied to new targets such as the Zika and Chikungunya viruses.
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Affiliation(s)
- Mauro Jorge Cabral-Castro
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marta Guimarães Cavalcanti
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Departamento de Doenças Infecciosas e Parasitárias, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marzia Puccioni-Sohler
- Laboratório de Líquido Cefalorraqueano, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Valéria Lima Carvalho
- Instituto Evandro Chagas, Seção de Arbovirologia e Febres Hemorrágicas, Ananindeua, Pará, Brazil
| | | | - José Mauro Peralta
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Domínguez CM, Kosaka PM, Mokry G, Pini V, Malvar O, del Rey M, Ramos D, San Paulo A, Tamayo J, Calleja M. Hydration induced stress on DNA monolayers grafted on microcantilevers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10962-10969. [PMID: 25148575 DOI: 10.1021/la501865h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex situ sequence identification does not require hybridization times typically longer than 1 h, while quantification is a major challenge.
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Affiliation(s)
- Carmen M Domínguez
- Instituto de Microelectrónica de Madrid, IMM-CNM (CSIC), 28760 Tres Cantos, Spain
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8
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Franssen-van Hal NLW, van der Putte P, Hellmuth K, Matysiak S, Kretschy N, Somoza MM. Optimized light-directed synthesis of aptamer microarrays. Anal Chem 2013; 85:5950-7. [PMID: 23672295 PMCID: PMC3686109 DOI: 10.1021/ac400746j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Aptamer microarrays are a promising
high-throughput method for
ultrasensitive detection of multiple analytes, but although much is
known about the optimal synthesis of oligonucleotide microarrays used
in hybridization-based genomics applications, the bioaffinity interactions
between aptamers and their targets is qualitatively different and
requires significant changes to synthesis parameters. Focusing on
streptavidin-binding DNA aptamers, we employed light-directed in situ
synthesis of microarrays to analyze the effects of sequence fidelity,
linker length, surface probe density, and substrate functionalization
on detection sensitivity. Direct comparison with oligonucleotide hybridization
experiments indicates that aptamer microarrays are significantly more
sensitive to sequence fidelity and substrate functionalization and
have different optimal linker length and surface probe density requirements.
Whereas microarray hybridization probes generate maximum signal with
multiple deletions, aptamer sequences with the same deletion rate
result in a 3-fold binding signal reduction compared with the same
sequences synthesized for maximized sequence fidelity. The highest
hybridization signal was obtained with dT 5mer linkers, and the highest
aptamer signal was obtained with dT 11mers, with shorter aptamer linkers
significantly reducing the binding signal. The probe hybridization
signal was found to be more sensitive to molecular crowding, whereas
the aptamer probe signal does not appear to be constrained within
the density of functional surface groups commonly used to synthesize
microarrays.
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Harrison A, Binder H, Buhot A, Burden CJ, Carlon E, Gibas C, Gamble LJ, Halperin A, Hooyberghs J, Kreil DP, Levicky R, Noble PA, Ott A, Pettitt BM, Tautz D, Pozhitkov AE. Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Res 2013; 41:2779-96. [PMID: 23307556 PMCID: PMC3597649 DOI: 10.1093/nar/gks1358] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
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Affiliation(s)
- Andrew Harrison
- University of Essex-Mathematical Sciences, Colchester CO4 3SQ, Essex, United Kingdom
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10
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Ozel AB, Srivannavit O, Rouillard JM, Gulari AE. Target concentration dependence of DNA melting temperature on oligonucleotide microarrays. Biotechnol Prog 2012; 28:556-66. [PMID: 22275183 DOI: 10.1002/btpr.1505] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 11/08/2011] [Indexed: 01/12/2023]
Abstract
The design of microarrays is currently based on studies focusing on DNA hybridization reaction in bulk solution. However, the presence of a surface to which the probe strand is attached can make the solution-based approximations invalid, resulting in sub-optimum hybridization conditions. To determine the effect of surfaces on DNA duplex formation, the authors studied the dependence of DNA melting temperature (T(m)) on target concentration. An automated system was developed to capture the melting profiles of a 25-mer perfect-match probe-target pair initially hybridized at 23°C. Target concentrations ranged from 0.0165 to 15 nM with different probe amounts (0.03-0.82 pmol on a surface area of 10(18) Å(2)), a constant probe density (5 × 10(12) molecules/cm(2)) and spacer length (15 dT). The authors found that T(m) for duplexes anchored to a surface is lower than in-solution, and this difference increases with increasing target concentration. In a representative set, a target concentration increase from 0.5 to 15 nM with 0.82 pmol of probe on the surface resulted in a T(m) decrease of 6°C when compared with a 4°C increase in solution. At very low target concentrations, a multi-melting process was observed in low temperature domains of the curves. This was attributed to the presence of truncated or mismatch probes.
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Affiliation(s)
- Ayse Bilge Ozel
- Dept. of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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11
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Trapp C, Schenkelberger M, Ott A. Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study. BMC BIOPHYSICS 2011; 4:20. [PMID: 22166491 PMCID: PMC3262748 DOI: 10.1186/2046-1682-4-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/13/2011] [Indexed: 01/29/2023]
Abstract
Background DNA is a carrier of biological information. The hybridization process, the formation of the DNA double-helix from single-strands with complementary sequences, is important for all living cells. DNA microarrays, among other biotechnologies such as PCR, rely on DNA hybridization. However, to date the thermodynamics of hybridization is only partly understood. Here we address, experimentally and theoretically, the hybridization of oligonucleotide strands of unequal lengths, which form a bulged loop upon hybridization. For our study we use in-house synthesized DNA microarrays. Results We synthesize a microarray with additional thymine bases in the probe sequence motifs so that bulged loops occur upon target hybridization. We observe a monotonic decrease of the fluorescence signal of the hybridized strands with increasing length of the bulged loop. This corresponds to a decrease in duplex binding affinity within the considered loop lengths of one to thirteen bases. By varying the position of the bulged loop along the DNA duplex, we observe a symmetric signal variation with respect to the center of the strand. We reproduce the experimental results well using a molecular zipper model at thermal equilibrium. However, binding states between both strands, which emerge through duplex opening at the position of the bulged loop, need to be taken into account. Conclusions We show that stable DNA duplexes with a bulged loop can form from short strands of unequal length and they contribute substantially to the fluorescence intensity from the hybridized strands on a microarray. In order to reproduce the result with the help of equilibrium thermodynamics, it is essential (and to a good approximation sufficient) to consider duplex opening not only at the ends but also at the position of the bulged loop. Although the thermodynamic parameters used in this study are taken from hybridization experiments in solution, these parameters fit our DNA microarray data well.
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Affiliation(s)
- Christian Trapp
- Experimentalphysik, Universität des Saarlandes, D-66041 Saarbrücken, Germany.
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Walter JC, Kroll KM, Hooyberghs J, Carlon E. Nonequilibrium effects in DNA microarrays: a multiplatform study. J Phys Chem B 2011; 115:6732-9. [PMID: 21542593 DOI: 10.1021/jp2014034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15 h in standard protocols (Hooyberghs et al. Phys. Rev. E2010, 81, 012901). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy ΔG with a slope equal to 1/RT(exp), where T(exp) is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of log I to ΔG/RT(eff). Here, T(eff) is an "effective" temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays [Hooyberghs et al. Phys. Rev. E2010, 81, 012901 and Hooyberghs et al. Nucleic Acids Res. 2009, 37, e53]. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.
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Affiliation(s)
- J-C Walter
- Institute for Theoretical Physics, KULeuven, Leuven, Belgium.
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Fasold M, Stadler PF, Binder H. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics 2010; 11:207. [PMID: 20423484 PMCID: PMC2884167 DOI: 10.1186/1471-2105-11-207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 04/27/2010] [Indexed: 02/02/2023] Open
Abstract
Background The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis. Results Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG)1-effect) are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG)1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes. We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN) model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms). Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data. Conclusions Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration algorithm for GeneChips which can be applied in a pre-correction step prior to standard preprocessing.
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Affiliation(s)
- Mario Fasold
- Interdisciplinary Centre for Bioinformatics, University Leipzig, Germany
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14
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Hooyberghs J, Baiesi M, Ferrantini A, Carlon E. Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:012901. [PMID: 20365418 DOI: 10.1103/physreve.81.012901] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Indexed: 05/29/2023]
Abstract
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs free-energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.
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Affiliation(s)
- J Hooyberghs
- Flemish Institute for Technological Research (VITO), Boeretang, B-2400 Mol, Belgium
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15
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Binder H, Fasold M, Glomb T. Mismatch and G-stack modulated probe signals on SNP microarrays. PLoS One 2009; 4:e7862. [PMID: 19924253 PMCID: PMC2775684 DOI: 10.1371/journal.pone.0007862] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/19/2009] [Indexed: 11/24/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested.
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Affiliation(s)
- Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany.
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