Evolution and characterization of a benzylguanine-binding RNA aptamer

Xu, Jin; Carrocci, Tucker J.; Hoskins, Aaron A.

doi:10.1039/c5cc07605f

Cited by 14 publications

(17 citation statements)

References 20 publications

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“…A different approach to producing a light-up aptamer is to bind and sequester a contact quencher covalently fused to a fluorophore, enabling easy switching of spectral properties by switching the fluorophore (Arora et al ., 2015). Finally, there is an aptamer that binds benzylguanine derivatives, enabling the use of SNAP-tag reagents to label RNAs, although these need to be washed out of the cell because they are fluorescent when unbound (Xu et al ., 2016). All of the aptamers described here require supplementation with an exogenous fluorophore.…”

Section: Tagging Of Nucleic Acidsmentioning

confidence: 99%

Genetically encoded fluorescent tags

Thorn

2017

MBoC

112

103

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Genetically encoded fluorescent tags are protein sequences that can be fused to a protein of interest to render it fluorescent. These tags have revolutionized cell biology by allowing nearly any protein to be imaged by light microscopy at submicrometer spatial resolution and subsecond time resolution in a live cell or organism. They can also be used to measure protein abundance in thousands to millions of cells using flow cytometry. Here I provide an introduction to the different genetic tags available, including both intrinsically fluorescent proteins and proteins that derive their fluorescence from binding of either endogenous or exogenous fluorophores. I discuss their optical and biological properties and guidelines for choosing appropriate tags for an experiment. Tools for tagging nucleic acid sequences and reporter molecules that detect the presence of different biomolecules are also briefly discussed.

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Section: Tagging Of Nucleic Acidsmentioning

confidence: 99%

Genetically encoded fluorescent tags

Thorn

2017

MBoC

112

103

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“…To further establish the proof-of-principle, the authors demonstrated that more complex structures provided more active RNAs (by examples of GTP-binding aptamers and ligase ribozymes) [ 112 ]. Notably, the hairpin motif derived in [ 58 ] was then successfully employed by other researchers to generate aptamers for different small-molecule targets [ 113 , 114 ].…”

Section: The Design Of Initial Na Libraries For More Affine Aptamementioning

confidence: 99%

Key Aspects of Nucleic Acid Library Design for in Vitro Selection

Vorobyeva

Davydova

Vorobjev

et al. 2018

IJMS

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Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.

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“…Finally, Xu et al developed an RNA aptamer that binds benzylguanine [ 23 ]. While benzylguanine is not a biologically-relevant DNA adduct, it is frequently used in place of O 6 -methylguanine for studies [ 37 ].…”

Section: Aptamers For Damaged Dnamentioning

confidence: 99%

Aptamers for DNA Damage and Repair

McKeague

2017

IJMS

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DNA is damaged on a daily basis, which can lead to heritable mutations and the activation of proto-oncogenes. Therefore, DNA damage and repair are critical risk factors in cancer, aging and disease, and are the underlying bases of most frontline cancer therapies. Much of our current understanding of the mechanisms that maintain DNA integrity has been obtained using antibody-based assays. The oligonucleotide equivalents of antibodies, known as aptamers, have emerged as potential molecular recognition rivals. Aptamers possess several ideal properties including chemical stability, in vitro selection and lack of batch-to-batch variability. These properties have motivated the incorporation of aptamers into a wide variety of analytical, diagnostic, research and therapeutic applications. However, their use in DNA repair studies and DNA damage therapies is surprisingly un-tapped. This review presents an overview of the progress in selecting and applying aptamers for DNA damage and repair research.

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Evolution and characterization of a benzylguanine-binding RNA aptamer

Cited by 14 publications

References 20 publications

Genetically encoded fluorescent tags

Genetically encoded fluorescent tags

Key Aspects of Nucleic Acid Library Design for in Vitro Selection

Aptamers for DNA Damage and Repair

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