Photoaffinity Labeling of Small‐Molecule‐Binding Proteins by DNA‐Templated Chemistry

Li, Gang; Liu, Ying; Liu, Yu; Chen, Li; Wu, Shao Peng; Liu, Yang; Li, Xiaoyu

doi:10.1002/anie.201302161

Cited by 101 publications

(99 citation statements)

References 66 publications

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“…Li and coworkers developed another method for assaying binding of small-molecules libraries to unmodified, non-immobilized proteins by DNA-programmed affinity labeling (DPAL) [21]. In DPAL (Figure 1c), unmodified proteins are mixed with small DNA oligonucleotides bearing a 5′ azidophenyl photocrosslinking moiety (PC-DNA).…”

Section: In Vitro Selection Methods For Ligand Discoverymentioning

confidence: 99%

Novel selection methods for DNA-encoded chemical libraries

Chan

McGregor

Liu

2015

Current Opinion in Chemical Biology

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Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.

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Section: In Vitro Selection Methods For Ligand Discoverymentioning

confidence: 99%

Novel selection methods for DNA-encoded chemical libraries

Chan

McGregor

Liu

2015

Current Opinion in Chemical Biology

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“…Based on this principle, we recently observed that mildly elevated salt concentration can indeed effectively suppress non-specific photo-crosslinking (Li et al 2013a). We examined the intermolecular photo-crosslinking between a DNA-based diazirine probe with BSA (bovine serum albumin), a protein well known for its extensive non-specific binding with diverse small molecules and widely used to block non-specific interactions (Avdulov et al 1996;Fielding et al 2005).…”

Section: The Salt Effectmentioning

confidence: 97%

“…Furthermore, we confirmed that this salt effect also works with non-DNA-based probes and probes with benzophenone and phenylazide, two other commonly used photo-crosslinkers. We have been applying this salt effect when characterizing small molecule-protein and DNAprotein interactions (Li et al 2013a(Li et al , 2014bLiu et al 2015).…”

Section: The Salt Effectmentioning

confidence: 98%

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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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“…Advances in automated DNA synthesis allowed the use of DNA as linker directly attached to the compound of interest. DNA-programmed photoaffinity labeling (DPAL) 26 is based on two complementary single stranded DNAs as depicted in Figure 1. A binding probe carries the small molecule attached to the DNA linker, while a capture probe consists of a photoreactive group attached to the complementary DNA.…”

Section: Entrymentioning

confidence: 99%