Immobilization of single-stranded DNA fragments to solid surfaces and their repeatable specific hybridization: covalent binding or adsorption?

Dugas, Vincent; Depret, Géraldine; Chevalier, Yves; Nesme, Xavier; Souteyrand, Éliane

doi:10.1016/j.snb.2004.02.041

Cited by 81 publications

(53 citation statements)

References 47 publications

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“…The crude product was purified by reversed-phase preparative HPLC to yield pure compound 22 (111 nmol), determined by spectrophotometry at 550 nm (e (Cy3) = 150 000). Fabrication of microarrays [12] Silanization of the glass slides: Borosilicate glass slides (Schott) containing 52 microreactors [38] (2 mm diameter, 65-100 mm deep) were functionalized by the protocol developed by Dugas et al [37] In brief, after piranha treatment, the slides were heated under dry nitrogen at 150 8C for 2 h. Next, dry pentane (250 mL) and tert-butyl-11-(dimethylamino)silylundecanoate (300 mL) were added at room temperature. After 20 min of incubation, the pentane was evaporated and the slides were heated at 150 8C overnight.…”

Section: Methodsmentioning

confidence: 99%

“…Accordingly, the 3'-amino-oligonucleotides, the sequence of which was complementary to that of the glycoconjugates prepared, were first covalently immobilized on functionalized [37] 52-well glass slides. [38] Then, the glycocluster oligonucleotide derivatives 22 and 23, the previously tested [12] galactosyl conjugates 24 a-d, and the additional galactosyl conjugate 25, which had ten galactose residues, were hybridized onto the chip in order to compare their lectin-binding properties.…”

Section: Synthesis and Characterization Of Glycoclusteroligonucleotidmentioning

confidence: 99%

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Design of Triazole‐Tethered Glycoclusters Exhibiting Three Different Spatial Arrangements and Comparative Study of their Affinities towards PA‐IL and RCA 120 by Using a DNA‐Based Glycoarray

et al. 2009

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Sugar-coated chips: Glycoside clusters are valuable tools for carbohydrate-lectin recognition studies. However, the spatial arrangement of the sugar residues is a key issue in the design of high-affinity glycoclusters. Here the affinities of linear and antenna- and calixarene-based galactoside clusters towards two lectins derived from Pseudomonas aeruginosa and Ricinus communis were compared by means of glycoarrays.Interactions between proteins and carbohydrates are involved in a large number of crucial biological events. Many efforts have been devoted to the design and synthesis of unnatural saccharides displaying high affinities towards targeted lectins. Among others, glycoside clusters have proven to be valuable tools for these recognition studies. However, the spatial arrangements of the sugar residues are a key issue in the design of high-affinity glycoclusters. Here, the affinities of linear and antenna- and calixarene-based galactoside clusters against two lectins, derived from Pseudomonas aeruginosa and Ricinus communis, have been compared by means of glycoarrays.

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Section: Methodsmentioning

confidence: 99%

Section: Synthesis and Characterization Of Glycoclusteroligonucleotidmentioning

confidence: 99%

Design of Triazole‐Tethered Glycoclusters Exhibiting Three Different Spatial Arrangements and Comparative Study of their Affinities towards PA‐IL and RCA 120 by Using a DNA‐Based Glycoarray

et al. 2009

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“…The fabrication of the DNA platform is detailed in , (Mazurczyk et al, 2008) and (Dugas et al, 2004). Details can also be found in the supplement information.…”

Section: Fabrication Of Microarraysmentioning

confidence: 99%

“…The Cy3 signal 05, 0.5, 1, 5, 100, 500, 1000, 2000, 3500, 6000, 9000, and 30,000 M. increases very slowly from 0.025 to 0.25 M, followed by a rapid increase of the relative surface density between 0.25 and 0.5 M leading to a plateau. Using 32 P labelled oligonucleotides, Dugas et al (Dugas et al, 2004) have demonstrated that the surface density of covalently immobilised amino-modified oligonucleotides was in the low 10 12 molecules cm −2 . These findings were confirmed by AFM observations (Lallemand et al, 2007).…”

Section: Influence Of Glycomimetic Concentration On the Hybridizationmentioning

confidence: 99%

DNA-directed immobilisation of glycomimetics for glycoarrays application: Comparison with covalent immobilisation, and development of an on-chip IC50 measurement assay

Zhang

Pourceau

Meyer

et al. 2009

Biosensors and Bioelectronics

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“…[32] The DNA anchoring platforms consisted of wells carrying either a complementary sequence of the conjugates for immobilization (S1) or a noncomplementary one (S2) as a control for nonspecific adsorptions. Fluorescence scanning of the Cy3 signal displayed a homogeneous hybridization of conjugates Scheme 1.…”

mentioning

confidence: 99%

DNA‐Based Carbohydrate Biochips: A Platform for Surface Glyco‐Engineering

et al. 2007

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Carbohydrates and glycoconjugates play a major role in key biological events such as cell-cell recognition, pathogenesis, and inflammation. [1,2] As a consequence, there is a need to understand the structural parameters governing the recognition of carbohydrates by their receptors. This knowledge will be of use for both fundamental research and potential applications in diagnostics or therapeutics. However, research in this field is slowed by the wide diversity of carbohydrate structures and by the minute amounts of materials available for experimentation. The design of sensitive and highthroughput technologies for the characterization of oligosaccharide/protein interactions [3] is therefore emerging as an attractive tool for chemists and biochemists. Available techniques such as isothermal calorimetry, enzyme-linked lectin assay, and even crystallographic studies provide data on carbohydrate/protein interactions, but they are often limited by the amount of available material.Carbohydrate microarray technology [4][5][6][7][8][9][10][11][12][13][14][15][16] is a promising approach for probing carbohydrate/protein interactions, and it permits the simultaneous screening of a number of biological interactions with only minute amounts of material. A large family of carbohydrate derivatives has been designed for immobilization on surfaces by various means. [5][6][7][8][9][10][11][12][13][14] However, this technology has various limitations. Relative surface densities of bound ligands are often not assessed. A careful optimization of the orientation and the distance separating the carbohydrate probe from the surface is often required.The interactions of oligosaccharides with lectins are usually weak (mm range) and can be enhanced using the "cluster effect" with multivalent ligands. [17][18][19][20] In the latter case, the distance between the residues should be optimized for binding. [21][22][23] Finally, the syntheses of functionalized oligosaccharide ligands are labor intensive.We report herein an original approach for the surface immobilization of oligosaccharides using glycoconjugate molecules that present a DNA sequence for anchoring onto DNA chips through hybridization. This approach has been used in the field of protein microarrays, [24,25] but to our knowledge this is the first time that such a strategy has been reported in the field of glycoarrays.Several syntheses of glycoconjugated oligonucleotides have been reported, but none are suitable for introducing different carbohydrate moieties. [26][27][28] We designed a conjugate that incorporates carbohydrate residue(s) for interacting with a lectin, an oligonucleotide sequence for anchoring on the surface, and a fluorescent tag at the 5'-end for the determination of relative surface densities (Figure 1). These moieties were assembled through a combination of automated oligonucleotide synthesis, and amidative oxidation and 1,3-dipolar cycloaddition ("click" chemistry) performed on a solid support (Scheme 1).[29] We introduced either one or three saccharide residue...

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Immobilization of single-stranded DNA fragments to solid surfaces and their repeatable specific hybridization: covalent binding or adsorption?

Cited by 81 publications

References 47 publications

Design of Triazole‐Tethered Glycoclusters Exhibiting Three Different Spatial Arrangements and Comparative Study of their Affinities towards PA‐IL and RCA 120 by Using a DNA‐Based Glycoarray

Design of Triazole‐Tethered Glycoclusters Exhibiting Three Different Spatial Arrangements and Comparative Study of their Affinities towards PA‐IL and RCA 120 by Using a DNA‐Based Glycoarray

DNA-directed immobilisation of glycomimetics for glycoarrays application: Comparison with covalent immobilisation, and development of an on-chip IC50 measurement assay

DNA‐Based Carbohydrate Biochips: A Platform for Surface Glyco‐Engineering

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