In vitro selection of aptamers that act with Zn2+

Kawakami, Junji; Imanaka, Hirofumi; Yokota, Yukie; Sugimoto, Naoki

doi:10.1016/s0162-0134(00)00158-6

Cited by 86 publications

(51 citation statements)

References 27 publications

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“…In 1990, Szostak's group (Ellington and Szostak, 1990) and Gold's group (Tuerk and Gold, 1990) developed an in vitro aptamer selection process from random sequence pool. Aptamers bind to a wide range of targets, including metal ions (Kawakami et al, 2000), metabolites (Bruno et al, 2008), proteins (Ruckman et al, 1998;Savla et al, 2011), and whole organisms, such as viruses (Tang et al, 2009), bacteria (Hamula et al, 2011) and mammalian cells (Chen et al, 2009). Aptamers have advantages as recognition molecules.…”

Section: Introductionmentioning

confidence: 99%

Screening and Characterization of a Novel RNA Aptamer That Specifically Binds to Human Prostatic Acid Phosphatase and Human Prostate Cancer Cells

Kong¹,

Byun²

2015

Molecules and Cells

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Section: Introductionmentioning

confidence: 99%

Screening and Characterization of a Novel RNA Aptamer That Specifically Binds to Human Prostatic Acid Phosphatase and Human Prostate Cancer Cells

Kong¹,

Byun²

2015

Molecules and Cells

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“…G-quadruplex | systematic evolution of ligands by exponential enrichment | sensor | binding induced folding | molecular recognition N ucleic acid-based aptamers (1,2) can be selected in vitro against a wide range of targets (3)(4)(5)(6)(7)(8), chemically modified and synthetically produced, thereby making them a promising class of molecules for many applications including diagnostics (9,10), in vivo imaging (11,12), and targeted therapeutics (13,14). Unlike most conventional affinity reagents (e.g., antibodies), aptamers can also be engineered to perform complex molecular functions beyond binding.…”

mentioning

confidence: 99%

In vitro selection of structure-switching, self-reporting aptamers

Plakos²,

Lou³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

119

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We describe an innovative selection approach to generate selfreporting aptamers (SRAs) capable of converting target-binding events into fluorescence readout without requiring additional modification, optimization, or the use of DNA helper strands. These aptamers contain a DNAzyme moiety that is initially maintained in an inactive conformation. Upon binding to their target, the aptamers undergo a structural switch that activates the DNAzyme, such that the binding event can be reported through significantly enhanced fluorescence produced by a specific stacking interaction between the active-conformation DNAzyme and a small molecule dye, N-methylmesoporphyrin IX. We demonstrate a purely in vitro selection-based approach for obtaining SRAs that function in both buffer and complex mixtures such as blood serum; after 15 rounds of selection with a structured DNA library, we were able to isolate SRAs that possess low nanomolar affinity and strong specificity for thrombin. Given ongoing progress in the engineering and characterization of functional DNA/RNA molecules, strategies such as ours have the potential to enable rapid, efficient, and economical isolation of nucleic acid molecules with diverse functionalities.G-quadruplex | systematic evolution of ligands by exponential enrichment | sensor | binding induced folding | molecular recognition N ucleic acid-based aptamers (1, 2) can be selected in vitro against a wide range of targets (3-8), chemically modified and synthetically produced, thereby making them a promising class of molecules for many applications including diagnostics (9, 10), in vivo imaging (11,12), and targeted therapeutics (13,14). Unlike most conventional affinity reagents (e.g., antibodies), aptamers can also be engineered to perform complex molecular functions beyond binding. For example, our group has recently demonstrated the use of an aptamer that undergoes target-binding-induced conformational change for continuous, real-time detection of a small molecule in undiluted blood serum (15). However, the selection process required to directly isolate aptamers with the desired function poses a significant technical challenge. One common approach entails selection for an aptamer on the basis of target binding, followed by postmodification and optimization through rational design in order to link the molecular binding capability to the desired functions (16,17). Unfortunately, such approaches rely upon prior knowledge of the threedimensional aptamer structure and require lengthy optimization steps that often compromise aptamers' affinity and specificity for their targets (18)(19)(20).Alternately, one can directly isolate aptamers with the desired function by combining a specifically designed nucleic acid library and a suitable selection process. For example, pioneering work by Nutiu and Li (21) described the isolation of structure-switching aptamers using a DNA library that was designed to incorporate two short randomized stretches sandwiching a central fixedsequence motif, with binding sites for two PCR...

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“…Aptamers are most commonly selected using a process known as systematic evolution of ligands by exponential enrichment (SELEX) [6], a screening technique involving the progressive selection of highly specific ligands from a large combinatorial nucleic acid library through repeated rounds of partition and amplification. Although aptamers for ions such as K 1 and Zn 21 and small molecules such as adenosine triphosphate (ATP) have been selected using SELEX [7,8], the processes are tedious and time-consuming. Due to the superior resolving power of CE, CE was demonstrated as an alternative SELEX selection procedure (CE-SELEX) [9].…”

Section: Introductionmentioning

confidence: 99%

Analysis of DNA complexes with small solutes by CE with LIF detection

2010

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In this article, we describe the analysis of aptamers for Hg(2+) ions through CE with LIF (CE-LIF) detection using 2% poly(ethylene oxide) solutions containing OliGreen (fluorophore). In the presence of an EOF, DNA strands migrating against the EOF were detected at the cathode end. Four DNA strands - T(33), T(5)C(28), T(5)C(5)T(23), and T(15)C(5)T(13) - could not be separated through CE-LIF in the absence of Hg(2+). At 0.3 mM Hg(2+), however, all four were partially separated within 20 min, with SDs of the migration times all being less than 2.5%. From the CE, fluorescence, and ellipticity data, we concluded that the conformations of these four DNA strands all changed from random-coil to folded structures as a result of T-Hg(2+)-T bonding. In addition, we found that this CE approach provided different electropherograms patterns for T(7), T(15), and T(33) in the absence and presence of Hg(2+), indicating various interactions of the DNA strands with Hg(2+). Using this simple, high-resolution CE approach, we also demonstrated that adenosine triphosphate has a stronger interaction with the adenosine triphosphate aptamer than with either the platelet-derived growth factor aptamer or T(33). This CE approach holds great potential for screening aptamers for small solutes, studying the catalytic activity of DNAzymes, and evaluating the biological functions of microRNA.

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In vitro selection of aptamers that act with Zn2+

Cited by 86 publications

References 27 publications

Screening and Characterization of a Novel RNA Aptamer That Specifically Binds to Human Prostatic Acid Phosphatase and Human Prostate Cancer Cells

Screening and Characterization of a Novel RNA Aptamer That Specifically Binds to Human Prostatic Acid Phosphatase and Human Prostate Cancer Cells

In vitro selection of structure-switching, self-reporting aptamers

Analysis of DNA complexes with small solutes by CE with LIF detection

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