Hybridization of DNA targets to glass-tethered oligonucleotide probes

Beattie, Wanda G.; Meng, Lin; Turner, Saralinda L.; Varma, Rajender S.; Dao, Dat D.; Beattie, Kenneth L.

doi:10.1007/bf02779015

Cited by 66 publications

(42 citation statements)

References 18 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

show abstract

“…ODNs can be prepared by automated synthesis and then immobilized on surfaces in an array using many different methods with varying degrees of efficiency [14,15,16,17]. Arrays can also be created by in situ photolithographic techniques [18].…”

Section: The Problems Associated With Present Methods Of Probe Densitmentioning

confidence: 99%

“…Glass, quartz, silicon, platinum and gold are all good surfaces for sequence analysis using ODN arrays and binding of ODN molecules to the surfaces is easily accomplished [3,4,5,6]. …”

mentioning

confidence: 99%

A Quantitative Tool for Producing DNA-Based Diagnostic Arrays

Whitaker¹

2008

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“…[58][59] The relative excess of DNA on the particle compared to the surface aids the chances of successful hybridisation. The exact number of bound molecules hybridising is difficult to estimate as it will be influenced by, among other things, particle curvature at the point of contact, crowding from other adjacent molecules, and exact density of the DNA on both the surface and the particle at the point of contact.…”

Section: Dna Binding Of Individual Nanoparticles To the Surfacementioning

confidence: 99%