Assessment of methods for covalent binding of nucleic acids to magnetic beads, DynabeadsTM, and the characteristics of the bound nucleic acids in hybridization reactions

Lund, Vera; Schmid, Ruth; Rickwood, D.; Robbiati, Federico Omar; Homes, Erik

doi:10.1093/nar/16.22.10861

Cited by 98 publications

(60 citation statements)

References 16 publications

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“…Therefore, very often functional/active groups are introduced to either the 3Ј-end or 5Ј-end of oligonucleotides and solid supports to allow end-specific immobilization. However, these functional groups often cause a high degree of nonspecific binding during attachment (9,17,26) and even hybridization (26). For example, it has been reported that nonspecific attachment and nonspecific hybridization of oligonucleotides occurs on both aminosilane-modified (9) and epoxysilane-modified (26) surfaces, which are the two most commonly used silane-modified surfaces for DNA array preparation.…”

Section: Discussionmentioning

confidence: 99%

Immobilization of Oligonucleotides onto a Glass Support via Disulfide Bonds: A Method for Preparation of DNA Microarrays

Rogers¹,

Jiang-Baucom²,

Huang³

et al. 1999

Analytical Biochemistry

239

158

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The covalent attachment of disulfide-modified oligonucleotides to a mercaptosilane-modified glass surface is described. This method provides an efficient and specific covalent attachment chemistry for immobilization of DNA probes onto a solid support. Glass slides were derivatized with 3-mercaptopropyl silane for attachment of 5-prime disulfide-modified oligonucleotides via disulfide bonds. An attachment density of approximately 3 ؋ 10 5 oligonucleotides/m 2 was observed. Oligonucleotides attached by this method provided a highly efficient substrate for nucleic acid hybridization and primer extension assays. In addition, we have demonstrated patterning of multiple DNA probes on a glass surface utilizing this attachment chemistry, which allows for array densities of at least 20,000 spots/cm 2 . © 1999 Academic Press Key Words: covalent immobilization; oligonucleotide; glass; disulfide bonds; DNA microarray.In recent years, high-density miniaturized oligonucleotide arrays have emerged as promising tools for assessing genomic data with a lower cost and higher throughput than the traditional gel-based methods. Such oligonucleotide arrays, or DNA chips, have been applied to genetic mutational scanning (1, 2), molecular bar coding (3), gene expression monitoring (4, 5), and sequencing (6 -8). The power of the DNA chips come from the highly parallel, addressable, miniaturized array format that provides significant advantages over traditional gel-based formats in terms of reagent cost, labor, speed, throughput, and operational simplicity. The development of efficient chemistries for the manufacture of spatially resolved, microscale DNA arrays on a solid-support is essential for the realization of the DNA chip technology potential. In most DNA chip applications, the DNA arrays are used to capture or analyze the target sequences and/or detection probes via hybridization reactions alone (1-7) or with subsequent primer extension reactions (8). The reliability and integrity of the hybridization reactions are highly dependent, in addition to the actual base composition of the arrayed oligonucleotides, on the quality and the characteristics of the DNA arrays. In developing a useful and reliable chemistry for producing DNA arrays, the accessibility and functionality of the surface-bound DNA, the density of attachment, the stability of the array, the reproducibility of the attachment chemistry, and the fidelity of the immobilized sequences are all critical.There have been numerous reports regarding immobilization (9 -26) or direct synthesis (27, 28) of oligonucleotides on solid supports, such as glass, silicon, membranes, and polystyrene. Parallel synthesis of oligonucleotides directly onto the solid support by photoactivatable chemistries (27) or standard phosphoramidite chemistries (28) have, thus far, been the most successful approach to manufacturing high-density DNA arrays. Patterning of presynthesized oligonucleotides, however, is preferred for many research applications and low-to moderate-density-array applications requi...

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Section: Discussionmentioning

confidence: 99%

Immobilization of Oligonucleotides onto a Glass Support via Disulfide Bonds: A Method for Preparation of DNA Microarrays

Rogers¹,

Jiang-Baucom²,

Huang³

et al. 1999

Analytical Biochemistry

239

158

View full text Add to dashboard Cite

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“…Covalent coupling is the most popular approach for immobilization of biomolecules. The solution-based binding kinetics has been extensively studied, making the coupling approach available for different applications [42,43]. Covalently coupled, probes are favorably presented on the surface of the bead, leaving the binding moieties available for interaction with target molecules.…”

Section: Surface Functionalization Of Microbeadsmentioning

confidence: 99%

Microfluidics for DNA and Protein Analysis with Multiplex Microbead-Based Assays

Yue

Yang

2016

Microfluidic Methods for Molecular Biology

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Early screening and diagnosis of diseases require the development of sensitive, reliable, and inexpensive high-throughput assays. There is a growing need for innovative diagnostic technologies that provide accurate detection of a broad range of diseases and enhance laboratory productivity. Developments in micro-and nanotechnology have advanced the "lab-on-a-chip" concept towards a new generation of point-of-care diagnostic devices that enable parallel detection of multiple analytes in small-volume samples with high sensitivity in a short time. These features fulfill some of the important criteria of bioanalysis used for biochemical studies, environmental analyses, and clinical diagnostics. However, the multiplexing capability of microfluidic-based assay is limited compared to conventional flow cytometric assays, particularly for encoded microbead-based assays, which are capable of simultaneously analyzing multiple analyte. It is possible to incorporate the microbead-based assays into microfluidic devices in order to retain all the advantages of the microdevice and significantly improve multiplexing capability. In this chapter, we summarize the latest development in microbeadbased assays and discuss the integration of the microbead technology with microfluidic devices. Applications of the integrated approach in multiplexed protein and DNA analysis are growing rapidly in the areas of biomarker research, cancer screening, and disease diagnosis. The prospects for future development and commercialization of these microbead-based microfluidic devices are also discussed.

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“…In a much earlier attempt to solve this problem, Lund et al (5) reported end-attachment of restricted DNA to a carboxylated magnetic beads using carbodiimide reagent at pH 7. The 5Ј-end of the DNA had been modified by attachment of a ␤-amino alkyl substituent, so attachment to the beads via an amide bond was assumed.…”

mentioning

confidence: 99%

Rapid SLT Gene Detection on Polyethylene–Coacrylic Acid Film without Molecular Labels or Surface-Fouling Agents

Zhang

Fawcett

Evans

et al. 2000

Analytical Biochemistry

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Assessment of methods for covalent binding of nucleic acids to magnetic beads, DynabeadsTM, and the characteristics of the bound nucleic acids in hybridization reactions

Cited by 98 publications

References 16 publications

Immobilization of Oligonucleotides onto a Glass Support via Disulfide Bonds: A Method for Preparation of DNA Microarrays

Immobilization of Oligonucleotides onto a Glass Support via Disulfide Bonds: A Method for Preparation of DNA Microarrays

Microfluidics for DNA and Protein Analysis with Multiplex Microbead-Based Assays

Rapid SLT Gene Detection on Polyethylene–Coacrylic Acid Film without Molecular Labels or Surface-Fouling Agents

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