Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection

Bearden, Samuel; Wang, Fanny; Hall, Adam R.

doi:10.1021/acs.analchem.9b01873

Cited by 14 publications

(10 citation statements)

References 55 publications

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“…Because these copies would no longer be methylated at CpG sites, they could artificially decrease the apparent fraction of methylated CpG sites in libraries from original template strands. Second, although the use of dual rather than single biotin should prevent dissociation of biotinylated copied strands from streptavidin during heating (19), any small fraction of copied strands that also come off the streptavidin beads during heat denaturation would contaminate the library with original molecules. Of several primers tested to specifically amplify the original molecules following bisulfite conversion, the one employed in the final protocol (Table S1; see Methods) performed best in preserving the expected methylation patterns, as described in Performance Evaluation 5 below.…”

Section: (Which Was Not Certified By Peer Review)mentioning

confidence: 99%

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

Wang

Douville

Cohen

et al. 2022

Preprint

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The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics in the future.

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Section: (Which Was Not Certified By Peer Review)mentioning

confidence: 99%

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

Wang

Douville

Cohen

et al. 2022

Preprint

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“…Biotin/streptavidin interactions are recognized as the strongest noncovalent interactions available in nature and have been extensively employed in the detection of target analytes in biomedical applications. [41][42][43] For this reason, this type of interaction is generally used to prove the applicability of a novel platform in the biosensing field. [44,45] We provide a dual-mode optical SA detection strategy based on a flexible, low-cost hydrogel nanocomposite (Scheme 1).…”

Section: Introductionmentioning

confidence: 99%

H³ (Hydrogel‐Based, High‐Sensitivity, Hybrid) Plasmonic Transducers for Biomolecular Interactions Monitoring

Miranda

Moretta

Dardano

et al. 2022

Adv Materials Technologies

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more complex systems, such as microelectronics and microfluidics, without compromising high sensitivity and mass production. [5] Among the many available polymeric materials, hydrogels represent the ideal substrates for plasmonic sensors due to their optical transparency, biocompatibility, and their swelling capability in presence of an aqueous environment. [6][7][8] Hydrogels are generally recognized as 3D architectures, whose crosslinking density, mesh network size, and polymerization agent can be tuned and selected according to the desired applications. Moreover, they can be easily engineered and made responsive to external stimuli, [9] this being crucial when designing analytical platforms with applications in biochemical sensing. [8,10] In this context, when properly assembled and functionalized, noble metal nanoparticles (NPs), basically silver (Ag), and gold (Au), represent the ideal transducers since they can show a dramatically high response upon exposure to a target analyte. In some cases, the transduction is visible to the naked eye, especially in liquid colorimetric assays, which exploit the capability of plasmonic nanoparticles to aggregate, undergoing deep color variations. [11][12][13] Even if very effective and similar to the Enzyme-Linked Immunosorbent Assay (ELISA) commercial kits, the liquid phase plasmonic assays could suffer from pH, ionic strength, and temperature both during the preparation of the assay and the measurement procedure itself. [14][15][16] To overcome these limitations without giving up the sensing advantages provided by plasmonic nanoparticles, both top-down and bottom-up fabrication strategies have been proposed to arrange them in periodic, quasiperiodic, and random arrays on different substrates. [17][18][19] Different transduction mechanisms have been proposed to design plasmonic biochemical sensors and to ensure high sensitivity and specificity. However, portability and ease of use of these optical devices still represent a hard-to-solve challenge. All these transduction mechanisms are based on the localized surface plasmon resonance (LSPR) exhibited by noble-metal NPs. [20,21] Refractometric biosensors exploit the LSPR shifts as a function of a target analyte when properly interacting with the biorecognition element adhered on the surface of the NPs; [22,23] Surface-enhanced infrared absorption (SEIRA) and surface-enhanced raman scattering (SERS) exploit the LSPR to enhance infrared and Raman signals of molecules onto plasmonic substrates; [24][25][26] Metal-enhanced fluorescence (MEF), also referred to as plasmon-enhanced fluorescence A hybrid plasmonic transducer made of a Poly-(ethylene glycol) diacrylate (PEGDA) hydrogel and citrate gold nanoparticles detects the biotin-streptavidin interaction at picomolar (× 10 −12 m ) concentrations. The all-solution fabrication strategy, herein proposed, is large-scale, easily tunable, and low-cost; nevertheless, this innovative device is highly reproducible and optically stable, and it can be used in dual-optical mode. Indeed, b...

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“…[11,12] This is so useful that biotin-streptavidin system has been widely used for the detection and localization observation of trace antigens, antibodies, viruses, and receptors. [13][14][15][16] The specific recognition between molecules and their corresponding receptor proteins plays an important role in clinical diagnosis and treatment, biomedicine, drug research and development. [17] Several methods have been used to study small ligands, protein receptors and their interactions.…”

Section: Introductionmentioning

confidence: 99%

Fluorometric Detection of Streptavidin with a Cationic Conjugated Polymer and Hairpin DNA Probe

Yan

Xiang

et al. 2021

ChemistrySelect

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A simple and rapid method for streptavidin (SA) detection is developed based on a cationic conjugated polymer (CCP)mediated fluorescence resonance energy transfer (FRET) between poly [(9,9-bis(6'-N, N, N-trimethylammonium) hexyl) fluorenylene phenylene (PFP) and SYBR Green I (SG I). A hairpin DNA labeled with biotin at the 3' terminus was designed for the binding of SA and SYBR Green I (SG I) so that an amplified signal of emission fluorescence was detected as the CCPmediated FRET was induced in the presence of SA. The calibration curve exhibited a linear correlation between fluorescence intensity and SA concentration from 0 to 40 nM, and the linear regression equation was y = 0.0467x + 0.5814, with a correlation coefficient (R 2 ) of 0.9927, and the detection limit was 0.5 nM. Further investigations showed that the method exhibited a significantly high specificity for the target protein and a satisfactory practical performance when human serum samples spiked with SA were tested. The results suggest that this strategy is practically applicable as it may enable an effective tool for studies on the ligand-protein interactions as well as the qualitative and quantitative detection of proteins.

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Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection

Cited by 14 publications

References 55 publications

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

H³ (Hydrogel‐Based, High‐Sensitivity, Hybrid) Plasmonic Transducers for Biomolecular Interactions Monitoring

Fluorometric Detection of Streptavidin with a Cationic Conjugated Polymer and Hairpin DNA Probe

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Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection

Cited by 14 publications

References 55 publications

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules

H3 (Hydrogel‐Based, High‐Sensitivity, Hybrid) Plasmonic Transducers for Biomolecular Interactions Monitoring

Fluorometric Detection of Streptavidin with a Cationic Conjugated Polymer and Hairpin DNA Probe

Contact Info

Product

Resources

About

H³ (Hydrogel‐Based, High‐Sensitivity, Hybrid) Plasmonic Transducers for Biomolecular Interactions Monitoring