Aptamer‐Based Affinity Labeling of Proteins

Vinkenborg, Jan L.; Mayer, Günter; Famulok, Michael

doi:10.1002/anie.201204174

Cited by 75 publications

(71 citation statements)

References 58 publications

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“…The Famulok group reported a strategy utilizing a phenyl azide as photo-cross-linker and validated the chemistry using three structurally different aptamers. 113 The Bertozzi group reported a proximity-enhanced biorthogonal ligation method for cross-linking between an aptamer conjugated to cyclooctyne and azidosu-gar-labeled glycoproteins. 114 Most recently, the Tan group reported a protein–aptamer template-directed cross-linking method with aptamers carrying an F-carboxyl group.…”

Section: Perspectivementioning

confidence: 99%

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

et al. 2017

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Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.

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Section: Perspectivementioning

confidence: 99%

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

et al. 2017

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“…It is necessary to have the DNA strand displacement process faster than the dissociation of the target from affinity ligands. This requirement can be achieved by using affinity ligands with slow dissociation rate, e.g., slow off-rate modified aptamer (SOMAmer); 10 stabilizing the binding complex by photo or chemical cross-linking; 11 and/or increasing the rate of intramolecular DNA strand displacement by tuning the length of DNA probes or increasing the incubation temperature. 12 …”

mentioning

confidence: 99%

Dynamic DNA Assemblies Mediated by Binding-Induced DNA Strand Displacement

et al. 2013

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Dynamic DNA assemblies, including catalytic DNA circuits, DNA nanomachines, molecular translators, and reconfigurable nanostructures, have shown promising potential to regulate cell functions, deliver therapeutic reagents, and amplify detection signals for molecular diagnostics and imaging. However, such applications of dynamic DNA assembly systems have been limited to nucleic acids and a few small molecules, due to the limited approaches to trigger the DNA assemblies. Herein, we describe a binding-induced DNA strand displacement strategy that can convert protein binding to the release of a predesigned output DNA at room temperature with high conversion efficiency and low background. This strategy allows us to construct dynamic DNA assembly systems that are able to respond to specific protein binding, opening an opportunity to initiate dynamic DNA assembly by proteins.

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“…The authors have successfully accomplished the inter-subunit crosslinking of egg-white avidin tetramer with this probe (Hatanaka et al 1994). Over the next two decades, covalent affinity probes have been extensively employed not only in target identification (Adam et al 2002b;Takaoka et al 2006;MacKinnon et al 2007;Ban et al 2010;Koteva et al 2010;Wurdak et al 2010;Eirich et al 2011;Cisar and Cravatt 2012;Park et al 2012;Shi et al 2012;Park et al 2013;Su et al 2013), but also in affinity labeling of proteins (Dorman and Prestwich 2000;Hatanaka and Sadakane 2002;Chen et al 2003;Hosoya et al 2004;Lee et al 2005;Koshi et al 2008; Tanaka et al Tsukiji et al 2009a;Das 2011;Wacker et al 2011;Wang et al 2011;Hayashi and Hamachi 2012;Tamura et al 2012;Vinkenborg et al 2012;Willems et al 2012) and activity-based proteomic profiling (ABPP) (Kozarich 2003;Chan et al 2004;Ballell et al 2005;Evans and Cravatt 2006;Sadaghiani et al 2007;Salisbury and Cravatt 2007;Cravatt et al 2008;Salisbury and Cravatt 2008;Uttamchandani et al 2008;Nomura et al 2010;…”

Section: Covalent Crosslinkingmentioning

confidence: 99%

“…proteins that bind to the crosslinker or the linker motif) (Wurdak et al 2010;Wu et al 2011). Therefore, it has become a dilemma in affinity purification when high probe concentration is desired for better capture of low abundance targets, but more probes will also lead to more non-specific captures (Chan et al 2004;Nakamura et al 2008;Sakurai et al 2012;Vinkenborg et al 2012). It is well known that high salt concentration can inhibit protein-DNA, protein-protein, and protein-matrix interactions in many biochemical applications such as immunoassays and immunohistochemical detections (Ha et al 1992;Misra et al 1994a, b;Lohman et al 1996;O'Brien et al 1998;Klenova et al 2002;Kalodimos et al 2004;Berggard et al 2007;Bertonati et al 2007).…”

Section: The Salt Effectmentioning

confidence: 99%

Affinity purification in target identification: the specificity challenge

Zheng

2015

Arch. Pharm. Res.

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Since phenotype-based screening directly evaluates capability of small molecules for modulating biology in actual biological systems, it has become an important discover modality in modern pharmaceutical sciences. However, in order to fully elucidate the molecular mechanism underlying the bioactivity of small molecules, identification of their biological targets is an indispensable step. Among the many target identification strategies developed during the past several decades, affinity purification remains to be one of the most important and powerful approaches, as it can directly reveal the physical interactions between small molecules and their biomolecular targets. However, due to the complexity of the proteome and the diversity of small molecule-protein interactions, affinity purification faces the specificity challenge: how to identify the true specific targets from the non-specific background? Focusing on this challenge, in this review, we briefly introduce the history and background of affinity purification, and then we discussed the major technological developments aiming to address this challenge. We have summarized these approaches in two categories: noise reduction and comparative distinction. This review also highlights the importance of choosing an integrated approach combining multiple methods to achieving success in target identification.

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Aptamer‐Based Affinity Labeling of Proteins

Cited by 75 publications

References 58 publications

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

Dynamic DNA Assemblies Mediated by Binding-Induced DNA Strand Displacement

Affinity purification in target identification: the specificity challenge

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