Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy

Peterlinz, Kevin A.; Georgiadis, R.; Herne, Tonya M.; Tarlov, Michael J.

doi:10.1021/ja964326c

Cited by 472 publications

(508 citation statements)

References 19 publications

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“…In a common method for the passivation of gold surfaces, ssDNA-SH-modified gold surfaces can be exposed to a solution containing a small-molecular-weight sulfanyl compound, such as mercapto hexanol or undecanol, which displaces most of the ssDNA-SH from the surface and forces the remaining ssDNA into an upright conformation. [66][67][68][69][70][71] Because this method is based on the substitution reaction between ssDNA-SH and sulfanyl-anchored small molecules, the decrease in the surface density of the ssDNA-SH is inevitable, resulting in low sensitivity for the constructed DNA-based sensor.…”

Section: Construction Of Oligodna/peg Hybrid Surfaces and Their Perfomentioning

confidence: 99%

Construction of a densely poly(ethylene glycol)-chain-tethered surface and its performance

Nagasaki

2011

Polym J

116

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Non-biofouling surfaces constitute one of the most important subjects in sensitively and selectively detecting biomolecular events. Poly(ethylene glycol) (PEG) chains tethered on substrate surfaces are well known to reduce non-biofouling characteristics. Protein adsorption onto a PEG-chain-tethered surface is strongly influenced by the density of the PEG chain and is almost completely suppressed by the successive treatment of longer PEG chains (5 kDa) followed by the treatment of PEG (2 kDa; mixed-PEG-chain-tethered surface) because of a significant increase in PEG chain density. To modify versatile substrate surface, PEG possessing pentaethylenehexamine at one end (N6-PEG) was prepared via a reductive amination reaction of aldehyde-ended PEG with pentaethylenehexamine. Using N6-PEG, antibody/PEG co-immobilization was conducted on a substrate possessing active ester groups. After the antibody was immobilized on the surface, PEG tethered chains were constructed surrounding the immobilized antibody. It is interesting to note that the PEG-chain-tethered functions not only as a non-fouling agent but also improves immune response. The hybrid surface was also applied to oligo DNA immobilization. The oligo DNA/PEG hybrid surface improved hybridization, retaining its non-fouling ability. Densely packed PEG tethered chains surrounding antibodies and/or oligo DNA improved their orientation on the surface. Thus, this material is promising as a high-performance biointerface for versatile applications. Keywords: antibody; biosensing; DNA; end-functionalized poly(ethylene glycol); enzyme-linked immunosorbent assay; hybrid biointerface; soft interface INTRODUCTION Specific biorecognition on substrate surfaces has long been utilized in many applications such as biosensing, 1 immunodiagnostics, 2 enzyme immunoassay, 3 western blotting 4 and protein microarrays. 5 Important factors for the improvement in specific biorecognition on surfaces are the suppression of nonspecific biofouling and the suitable orientation of immobilized biomolecules. The former decreases nonspecific noise and the background level, and the latter increases the specific recognition level. To improve the non-biofouling character of surfaces, numerous efforts have been undertaken. In general, natural polymers such as albumin, casein and dextran have been used for blocking on substrate surfaces. 6 These treatments work well and suppress protein biofouling extensively. If extremely high performance is required, however, these blocking treatments are not enough. In addition, natural products, especially those derived from animals, may have undesired contents such as bacteria and viruses, which may affect the user. 7 Under these circumstances, synthetic polymers have been recently suggested as suitable surface blocking agents. Numerous types of water-soluble polymers, such as poly(acrylamide), poly(vinyl alcohol), poly(vinyl pyrrolidone) and poly(ethylene glycol) (PEG), have been investigated so far. Recently, new types of synthetic polymers such as poly(methoxy ...

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Section: Construction Of Oligodna/peg Hybrid Surfaces and Their Perfomentioning

confidence: 99%

Construction of a densely poly(ethylene glycol)-chain-tethered surface and its performance

Nagasaki

2011

Polym J

116

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“…Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24] However, constructing a reproducible DNA recognition layer with both of these properties is a critical challenge owing to unexpected surface adsorptions, disordered conformations, inconsistencies in grafting density and the flexibility of probe molecules. It is thus imperative to obtain an in-depth understanding of the factors that influence the structure of immobilized DNA layers.…”

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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In addition to its fundamental function as a genetic code carrier, the utilization of DNA in various material applications has been actively explored over the past several decades. DNA is intrinsically an excellent type of self-assembly nanomaterial owing to its predictable base-pairing, high chemical stability and the convenience it possesses for synthesis and modification. Because of these unparalleled properties, DNA is widely used as excellent recognition elements in biosensors and as unique building blocks in nanodevices. A critical challenge in surface-based DNA biosensors lies in the reduced accessibility of target molecules to the DNA probes arranged on heterogeneous surfaces, especially when compared to probe-target recognition in homogeneous solutions. To improve the recognition abilities of these heterogeneous surface-confined DNA probes, much effort has been devoted to controlling the surface chemistry, conformation and packing density of the probe molecules, as well as the size and geometry of the surface. In this review, we aim to summarize the recent progress on the improvement of the probetarget recognition properties by introducing DNA nanostructure scaffolds. A range of new strategies have proven to provide a significantly enhanced range in the spatial positioning and the accessibility of the probes to the surface over previously reported linear structures. We will also describe the applications of DNA nanostructure scaffold-based biosensors. INTRODUCTIONDetection of nucleic acids (DNA or RNA) is an integral step in many applications, including in clinical diagnosis, environmental monitoring and antibioterrorism. 1 With these applications in mind, significant efforts have been made to develop sensitive, selective, rapid and cost-effective DNA (or RNA) biosensors. In parallel, DNAbased devices have also attracted a significant, recent interest owing to their promising applications in nanoelectronics, 2,3 biomolecular computations, 4-8 cellular imaging 9 and drug delivery. [10][11][12] In a typical design of DNA biosensors and nanodevices, oligonucleotides are often used as the molecular recognition layer. Because DNA is comprised of only four bases with A-T and G-C pairing, DNA hybridization processes are highly predictable and can be finely tuned with a rational design of the sequence. In addition, DNA oligonucleotides are usually easy to design, chemically stable and cost-effective.Understanding the physical structure of a DNA probe immobilized on a surface is critical in applications using DNA as a molecular recognition element. The properties of the DNA molecular recognition layer (such as selectivity, sensitivity and reproducibility) highly depend on the structure of the self-assembled DNA film. Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24]

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“…The complementary ss-DNA strand modified at the 5Ј end by a HO͑CH 2 ͒ 6 S-S͑CH 2 ͒ 6 tether for adsorption on Au termed RS-O20 was purchased from metabion ͑Martinsried, Germany͒. [34][35][36][37][38] The structures of CofCn-O5, CofCn-O20, and RS-O20 are depicted in Fig. 2.…”

Section: A Preparation Of Flavin-dna-disulfide Ligands and Protein Ementioning

confidence: 99%

“…The hybridization of DNA at the solid phase is a more complex process than in solution. 36,43 However, the base sequence was chosen to allow hybridization at room temperature only when complete overlap of the complementary ss-DNA strands is guaranteed. Efficient hybridization could be recorded after addition of CofC4-O20 to the complementary Au-S-O20 monolayer.…”

Section: B Tarlov Proceduresmentioning

confidence: 99%

Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers

et al. 2008

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Dodecin from Halobacterium salinarum is a dodecameric, hollow-spherical protein, which unspecifically adopts flavin molecules. Reduction of flavin dodecin holocomplexes induces dissociation into apododecin and free flavin. Unspecific binding and dissociation upon reduction were used as key properties to construct an electrochemically switchable surface, which was able to bind and release dodecin apoprotein depending on the applied potential. A flavin modified electrode surface ͑electrode-DNA-flavin͒ was generated by direct adsorption of double stranded DNA ͑ds-DNA͒ equipped with flavin and disulfide modifications at opposite ends. While the disulfide functionality enabled anchoring the ds-DNA at the gold surface, the flavin exposed at the surface served as the redox-active dodecin docking site. The structures of protein and flavin-DNA hybrid ligands were optimized and characterized by x-ray structural analysis of the holocomplexes. By surface plasmon resonance ͑SPR͒ spectroscopy, the adsorption of flavin modified DNA as well as the binding and the electrochemically induced release of dodecin apoprotein could be shown. When the surface immobilization protocol was changed from direct immobilization of the modified ds-DNA to a protocol, which included the hybridization of flavin and thiol modified DNA at the surface, the resulting monolayer was electrochemically inactive. A possible explanation for the strong influence of the surface immobilization protocol on addressing dodecin by the applied potential is that electron transfer is rather mediated by defects in the monolayer than modified ds-DNA.

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Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy

Cited by 472 publications

References 19 publications

Construction of a densely poly(ethylene glycol)-chain-tethered surface and its performance

Construction of a densely poly(ethylene glycol)-chain-tethered surface and its performance

Scaffolded biosensors with designed DNA nanostructures

Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers

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