Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates

Mavrogiannopoulou, E.; Petrou, Panagiota; Koukouvinos, Georgios; Yannoukakos, Drakoulis; Siafaka-Kapadai, Athanassia; Fornal, K.; Awsiuk, Kamil; Budkowski, Andrzej; Kakabakos, Sotirios

doi:10.1016/j.colsurfb.2015.02.045

Cited by 10 publications

(5 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Surface-immobilized oligonucleotide capture probes via the biotin–streptavidin interaction are used in a variety of applications. − The quality of capture probes binding to a surface has a massive influence on the sensitivity and specificity of the assay. Our group works on the development of screening technologies including multiplex hybridization and PCR assays.…”

Section: Resultsmentioning

confidence: 99%

“…The most obvious solution for high hybridization efficiencies is regioselective coupling that allows for the binding of oligonucleotides to the surface with the desired end . Biotinylation of oligonucleotides with subsequent binding to streptavidin (SA), or to its homologues, is one of the most used regioselective binding methods, owing to its stability, efficiency, and ease of use and high relevance for numerous studies. − This bond is suitable for use with oligonucleotides and oligonucleotide probes with hybridization efficiencies >90%.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

et al. 2020

View full text Add to dashboard Cite

One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10–15 μm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH–biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH–biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The microarray based systems, in particular the MIDTAL system, show great promise to allow for detection of a high number of HAS in-tandem. The main disadvantage of such microarrays is detection sensitivity, however, a number of strategies may be employed to increase such sensitivity [41,42]. Other disadvantages, such as sample extraction and handling, may be addressed through the use of automated microfluidics [43].…”

Section: Biosensors To Detect Harmful Algal Speciesmentioning

confidence: 99%

Biosensors for the monitoring of harmful algal blooms

McPartlin

Loftus

Crawley

et al. 2017

Current Opinion in Biotechnology

View full text Add to dashboard Cite

Harmful algal blooms (HABs) are a major global concern due to their propensity to cause environmental damage, healthcare issues and economic losses. In particular, the presence of toxic phytoplankton is a cause for concern. Current HAB monitoring programs often involve laborious laboratory-based analysis at a high cost and with long turnaround times. The latter also hampers the potential to develop accurate and reliable models that can predict HAB occurrence. However, a promising solution for this issue may be in the form of remotely deployed biosensors, which can rapidly and continuously measure algal and toxin levels at the point-of-need (PON), at a low cost. This review summarises the issues HABs present, how they are difficult to monitor and recently developed biosensors that may improve HAB-monitoring challenges.

show abstract

“…The streptavidin–biotin binding system has unique properties, enabling formation of bridges between the surface and biotin-labeled biomolecules, − rendering them more accessible for reaction with their counterpart molecules in the reaction mixture. Thus, it has been employed to immobilize biotinylated oligonucleotide probes onto surfaces, leading not only to immobilization of a high oligonucleotide amount but also to excellent spot repeatability of size and shape. , Biotin–streptavidin linkage has been also used to immobilize antibodies in a controlled manner, enhancing the analytical sensitivity of the immunoassay developed using these antibodies as compared to that developed employing randomly biotinylated ones . Additionally, Magliulo et al presented a biosensor based on OFET enabling detection of biotin at the low part per trillion concentration level .…”

Section: Introductionmentioning

confidence: 99%

“…Thus, it has been employed to immobilize biotinylated oligonucleotide probes onto surfaces, 25 leading not only to immobilization of a high oligonucleotide amount but also to excellent spot repeatability of size and shape. 23,24 Biotin−streptavidin linkage has been also used to immobilize antibodies in a controlled manner, 26 enhancing the analytical sensitivity of the immunoassay developed using these antibodies as compared to that developed employing randomly biotinylated ones. 27 Additionally, Magliulo et al presented a biosensor based on OFET enabling detection of biotin at the low part per trillion concentration level.…”

Section: Introductionmentioning

confidence: 99%

Orientation of Biotin-Binding Sites in Streptavidin Adsorbed onto the Surface of Polythiophene Films

et al. 2019

View full text Add to dashboard Cite

The orientation of biotin-binding sites of streptavidin adsorbed to thin films of three polythiophenes (PTs), namely, regioregular poly(3-hexylthiophene) (RP3HT), regiorandom poly(3-butylthiophene) (P3BT), and poly(3,3‴-didodecylquaterthiophene) (PQT12), has been investigated. Polymer films were examined prior to and after protein adsorption with atomic force microscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Principal component analysis (PCA) applied to ToF-SIMS data revealed subtle changes in surface chemistry of polymer films and orientation of adsorbed streptavidin. PCA resolved the surface alignment of alkyl side chains and differentiated the ToF-SIMS data for PQT12, RP3HT, and P3BT, verifying an amorphous morphology for P3BT and a semicrystalline one for PQT12 and RP3HT. After the characterization of the polymeric films, streptavidin adsorption from solutions with different protein concentrations (up to 300 μg/mL) has been conducted. The PCA results distinguished between amino acids characteristic for external regions of streptavidin molecules adsorbed to different PTs suggest that streptavidin adsorbed to PQT12 exposes molecular regions rich in tryptophan and tyrosine, which are components of the biotin-binding sites. The latter results were confirmed using biotin-labeled horse radish peroxidase to estimate the exposed binding sites of streptavidin adsorbed onto the different PT films. The analysis of streptavidin structure suggests that interaction between polythiophene film and dipole moment of streptavidin subunit is responsible for orientation of biotin-binding sites.

show abstract

Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates

Cited by 10 publications

References 44 publications

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures

Biosensors for the monitoring of harmful algal blooms

Orientation of Biotin-Binding Sites in Streptavidin Adsorbed onto the Surface of Polythiophene Films

Contact Info

Product

Resources

About