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Haug R, Kramer M, Richert C. Three-pronged probes: high-affinity DNA binding with cap, β-alanines and oligopyrrolamides. Chemistry 2014; 19:15822-6. [PMID: 24222391 DOI: 10.1002/chem.201302972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
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2
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Minuth M, Richert C. A nucleobase analogue that pairs strongly with adenine. Angew Chem Int Ed Engl 2013; 52:10874-7. [PMID: 24038815 DOI: 10.1002/anie.201305555] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Marco Minuth
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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4
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Vogel H, Richert C. Labeling Small RNAs through Chemical Ligation at the 5′ Terminus: Enzyme-Free or Combined with Enzymatic 3′-Labeling. Chembiochem 2012; 13:1474-82. [DOI: 10.1002/cbic.201200214] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Indexed: 01/01/2023]
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Gunnarsson A, Sjövall P, Höök F. Liposome-based chemical barcodes for single molecule DNA detection using imaging mass spectrometry. NANO LETTERS 2010; 10:732-737. [PMID: 20085369 DOI: 10.1021/nl904208y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on a mass-spectrometry (time-of-flight secondary ion mass spectrometry, TOF-SIMS) based method for multiplexed DNA detection utilizing a random array, where the lipid composition of small unilamellar liposomes act as chemical barcodes to identify unique DNA target sequences down to the single molecule level. In a sandwich format, suspended target-DNA to be detected mediates the binding of capture-DNA modified liposomes to surface-immobilized probe-DNA. With the lipid composition of each liposome encoding a unique target-DNA sequence, TOF-SIMS analysis was used to determine the chemical fingerprint of the bound liposomes. Using high-resolution TOF-SIMS imaging, providing sub-200 nm spatial resolution, single DNA targets could be detected and identified via the chemical fingerprint of individual liposomes. The results also demonstrate the capability of TOF-SIMS to provide multiplexed detection of DNA targets on substrate areas in the micrometer range. Together with a high multiplexing capacity, this makes the concept an interesting alternative to existing barcode concepts based on fluorescence, Raman, or graphical codes for small-scale bioanalysis.
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Affiliation(s)
- Anders Gunnarsson
- Department of Applied Physics, Division of Biological Physics, Chalmers University of Technology, Göteborg, Sweden
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Hong M, Zhou X, Li J, Tian Y, Zhu J. Nanoscale Architecture Dictates Detection Profile of Surface-Confined DNA by MALDI-TOF MS. Anal Chem 2009; 81:8839-45. [DOI: 10.1021/ac901815v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Min Hong
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Xin Zhou
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jiping Li
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Yuan Tian
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jin Zhu
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
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Printz M, Richert C. Pyrenylmethyldeoxyadenosine: A 3′-Cap for Universal DNA Hybridization Probes. Chemistry 2009; 15:3390-402. [DOI: 10.1002/chem.200801587] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Qiu F, Jiang D, Ding Y, Zhu J, Huang L. Monolayer-Barcoded Nanoparticles for On-Chip DNA Hybridization Assay. Angew Chem Int Ed Engl 2008; 47:5009-12. [DOI: 10.1002/anie.200800435] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Qiu F, Jiang D, Ding Y, Zhu J, Huang L. Monolayer-Barcoded Nanoparticles for On-Chip DNA Hybridization Assay. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Casneuf T, Van de Peer Y, Huber W. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics 2007; 8:461. [PMID: 18039370 PMCID: PMC2213692 DOI: 10.1186/1471-2105-8-461] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 11/26/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. RESULTS We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. CONCLUSION The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
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Affiliation(s)
- Tineke Casneuf
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium.
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Abstract
The high fidelity detection of multiple DNA sequences in multiplex assays calls for duplexes whose stability is independent of sequence (isostable DNA), forming under universally stringent conditions. Nature did not evolve DNA to form isostable duplexes. Here we report how probe strands can be modified so that an all-A/T target strand is bound with the same or slightly higher affinity than the corresponding all-G/C strand with the same sequence of purines and pyrimidines. We refer to these probes that feature covalently attached ligands as "decorated nucleic acids". Caps, intercalators, and locks were used to stabilize A/T duplexes, and N4-ethylcytosine residues were employed to tune down the stability of G/C duplexes without significantly affecting base pairing selectivity. Near-isostability was demonstrated in solution and on microarrays of high and low density. Further, it is shown that hybridization results involving decorated probes on microarrays can be predicted on the basis of thermodynamic data for duplex formation in solution. Predictable formation of isostable DNA not only benefits microarrays for gene expression analysis and genotyping, but may also improve the sequence-specificity of other applications that rely on the massively parallel formation of Watson-Crick duplexes.
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Affiliation(s)
- Carolin Ahlborn
- Institut für Organische Chemie, Universität Karlsruhe (TH), Karlsruhe, Germany
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12
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Plutowski U, Vogel SR, Bauer M, Deck C, Pankratz MJ, Richert C. Enzyme-free interrogation of RNA sites via primers and oligonucleotides 3'-linked to gold surfaces. Org Lett 2007; 9:2187-90. [PMID: 17480088 DOI: 10.1021/ol070724g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of a phosphoramidite is described that was used for the preparation of oligonucleotides with a 3'-terminal thiol, linked to the DNA via a SAM-forming undecyl chain and a nonadsorptive tetraethylene glycol unit. A gold surface featuring oligonucleotide probes allowed for label-free in situ mass spectrometric determination of a nucleotide in subpicomole quantities of an RNA transcript.
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Affiliation(s)
- Ulrich Plutowski
- Institute of Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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13
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Hagenbuch P, Kervio E, Hochgesand A, Plutowski U, Richert C. Chemical primer extension: efficiently determining single nucleotides in DNA. Angew Chem Int Ed Engl 2006; 44:6588-92. [PMID: 16175646 DOI: 10.1002/anie.200501794] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Patrizia Hagenbuch
- Institut für Organische Chemie, Universität Karlsruhe TH, 76131 Karlsruhe, Germany
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14
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Becker CFW, Wacker R, Bouschen W, Seidel R, Kolaric B, Lang P, Schroeder H, Müller O, Niemeyer CM, Spengler B, Goody RS, Engelhard M. Direct readout of protein-protein interactions by mass spectrometry from protein-DNA microarrays. Angew Chem Int Ed Engl 2006; 44:7635-9. [PMID: 16245381 DOI: 10.1002/anie.200502908] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian F W Becker
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Becker CFW, Wacker R, Bouschen W, Seidel R, Kolaric B, Lang P, Schroeder H, Müller O, Niemeyer CM, Spengler B, Goody RS, Engelhard M. Direkter Nachweis von Protein-Protein-Wechselwirkungen durch Massenspektrometrie an Protein-DNA-Mikroarrays. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200502908] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Hagenbuch P, Kervio E, Hochgesand A, Plutowski U, Richert C. Chemical Primer Extension: Efficiently Determining Single Nucleotides in DNA. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1110-21. [PMID: 16106339 DOI: 10.1002/jms.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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Abstract
One of the critical problems in the short oligo microarray technology is how to deal with cross-hybridization that produces spurious data. Little is known about the details of cross-hybridization effect at molecular level. Here, we report a free energy analysis of cross-hybridization on short oligo microarrays using data from a spike-in study. Our analysis revealed that cross-hybridization on the arrays is mostly caused by oligo fragments with a run of 10–16 nt complementary to the probes. Mismatches were estimated to be energetically much more costly in cross-hybridization than that in gene-specific hybridization, implying that the sources of cross-hybridization must be very different between a PM–MM probe pair. Consequently, it is unreliable to use MM probe signal to track cross-hybridizing signal on a corresponding PM probe. Our results also showed that the oligo fragments tend to bind to the 5′ ends of the probes, and are rarely seen at the 3′ ends. These results are useful for microarray design and data analysis.
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Affiliation(s)
| | - Roberto Carta
- Department of Statistic and Actuarial Sciences, University of Central FloridaOrlando, FL 32816–2370, USA
| | - Li Zhang
- To whom correspondence should be addressed. Tel: +1 713 563 4298; Fax: +1 713 563 4243;
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