New highly sensitive and selective catalytic DNA biosensors for metal ions

Lu, Yi; Liu, Juewen; Li, Jing; Bruesehoff, Peter J.; Pavot, Caroline M.-B.; Brown, Adam R.

doi:10.1016/s0956-5663(03)00013-7

Cited by 128 publications

(93 citation statements)

References 142 publications

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“…273 Many different types of combinatorial methods have been already employed to obtain new sensitive optical probes. 110,[273][274][275][276][277][278][279][280][281][282] Solid-phase organic synthesis is a well-established tool for the production of combinatorial libraries, but it has been mainly used for drug discovery. Resin bound chemosensors for several analytes have been made by combinatorial methods.…”

Section: Nanosensorsmentioning

confidence: 99%

Design of fluorescent materials for chemical sensing

2007

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There is an enormous demand for chemical sensors for many areas and disciplines. High sensitivity and ease of operation are two main issues for sensor development. Fluorescence techniques can easily fulfill these requirements and therefore fluorescent-based sensors appear as one of the most promising candidates for chemical sensing. However, the development of sensors is not trivial; material science, molecular recognition and device implementation are some of the aspects that play a role in the design of sensors. The development of fluorescent sensing materials is increasingly captivating the attention of the scientists because its implementation as a truly sensory system is straightforward. This critical review shows the use of polymers, sol-gels, mesoporous materials, surfactant aggregates, quantum dots, and glass or gold surfaces, combined with different chemical approaches for the development of fluorescent sensing materials. Representative examples have been selected and they are commented here.

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Section: Nanosensorsmentioning

confidence: 99%

Design of fluorescent materials for chemical sensing

2007

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“…in the case of the hammerhead ribozyme [45][46][47]. In addition, there are several examples of both naturally occurring and in vitro designed ribozymes and DNAzymes [8,[48][49][50][51][52], which show a fast decrease in reaction kinetics if trace amounts of other metal ions are present aside from the inherent one. It is therefore evident that not only Mg 2+ but other metal ions as well need to be considered in order to understand the structure and functioning of nucleic acids in general, and of ribozymes specifically.…”

Section: +mentioning

confidence: 99%

From nucleotides to ribozymes—A comparison of their metal ion binding properties

Freisinger

Sigel

2007

Coordination Chemistry Reviews

155

181

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It is undisputable that the fates of metal ions and nucleic acids are inescapably interwoven. Metal ions are essential for charge compensation of the negatively charged phosphate-sugar backbone, they are instrumental for proper folding, and last but not least they are crucial cofactors for ribozyme catalysis. Considerable progress has been achieved in the past few years on the identification of metal ion binding sites in large DNA and RNA molecules, like in ribozymes including the ribosome. Hereby, most information was gained from crystallography, which fails to explain metal ion binding equilibria in solution as well as the factors that determine the coordination of a metal ion to a specific site. In contrast, such information is readily available for the low-molecular building blocks of large nucleic acids, i.e. for mononucleotides and to some extent also dinucleotides. In this review, we combine and compare for the first time both sets of information. The focus is thereby set on Mg2+, Ca2+, Mn2+, and Cd2+ because these four metal ions are either freely available in cells, have a large impact on the catalytic rate of ribozymes, and/or are often applied in RNA biochemistry. Our comparisons show that results obtained from small molecules can be directly transposed to the findings in large RNA structures like the ribosome. For example, the basic coordination-chemical properties of the different metal ions are reflected in their binding to large nucleic acid structures: macrochelate formation, e.g. the simultaneous intranucleotide coordination of a Mg2+ ion to the phosphate unit and the N7 site of a purine nucleobase (be it inner-or outersphere), is well known for mononucleotides. We show that the frequency of occurrence of this type of coordination is the same for mononucleotides and the ribosome.

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“…Most DNAzymes require metal ion cofactors for structure and function, and many DNAzymes show high metal-binding affinity and specificity (33)(34)(35)(36)(37)(38). For example, the 8-17 DNAzyme can be activated by a trace amount of Pb 2ϩ (39), and it has been transformed into sensors for Pb 2ϩ (39)(40)(41)(42). Despite the initial success, no metal sensor has reached the detection limit and selectivity of instrumental analysis.…”

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confidence: 99%

A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity

Liu

Brown

Meng

et al. 2007

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

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482

476

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Here, we report a catalytic beacon sensor for uranyl (UO 2 2؉ ) based on an in vitro-selected UO 2 2؉ -specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3 quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5 and 3 ends, respectively. The presence of UO 2 2؉ causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of Ϸ230 M. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.DNA ͉ DNAzyme ͉ fluorescence ͉ deoxyribozyme ͉ catalytic DNA

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New highly sensitive and selective catalytic DNA biosensors for metal ions

Cited by 128 publications

References 142 publications

Design of fluorescent materials for chemical sensing

Design of fluorescent materials for chemical sensing

From nucleotides to ribozymes—A comparison of their metal ion binding properties

A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity

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