15N−15N J-Coupling Across HgII:  Direct Observation of HgII-Mediated T−T Base Pairs in a DNA Duplex

Hydrogels are crosslinked hydrophilic polymer networks with low optical background and high loading capacity for immobilization of biomolecules. Importantly, the property of hydrogel can be precisely controlled by changing the monomer composition. This feature, however, has not been investigated in the rational design of hydrogel-based optical sensors. We herein explore electrostatic interactions between an immobilized mercury binding DNA, a DNA staining dye (SYBR Green I), and the hydrogel backbone. A thymine-rich DNA was covalently functionalized within monolithic hydrogels containing a positive, neutral, or negative backbone. These hydrogels can be used as sensors for mercury detection since the DNA can selectively bind Hg 2+ between thymine bases inducing a hairpin structure. SYBR Green I can This document is the Accepted Manuscript version of a Published Work that appeared in final form in Applied Materials and Interfaces, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/am101068c2 then bind to the hairpin to emit green fluorescence. For the neutral or negatively charged gels, addition of the dye in the absence of Hg 2+ resulted in intense yellow background fluorescence, which was attributed to SYBR Green I binding to the unfolded DNA. We found that by introducing 20% positively charged allylamine monomer, the background fluorescence was significantly reduced. This was attributed to the repulsion between positively charged SYBR Green I by the gel matrix as well as the strong binding between the DNA and the gel backbone. The signal-to-background ratio and detection limit was respectively improved by six and nine-fold using the cationic gel instead of neutral polyacrylamide gel.This study helps understand the electrostatic interaction within hydrogels, showing that hydrogels can not only serve as a high capacity matrix for sensor immobilization, but can also actively influence the interaction between involved molecules.

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“…This DNA is rich in thymine and Hg 2+ can be selectively chelated by thymines to fold the DNA into a hairpin (23).…”

Section: Introductionmentioning

confidence: 99%

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg²⁺ Detection

Joseph

Dave

Liu

2011

ACS Appl. Mater. Interfaces

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“…Incorporation of 15 N labeled thymine nucleobases allowed the first direct spectroscopic proof of such T-Hg 2+ -T base pairs: 15 N NMR studies revealed a 15 N-15 N J-coupling across the Hg 2+ ion (see Section 5). [51] A highly selective oligodeoxyribonucleotide Hg 2+ sensor could be created based on this specific interaction. [52,53] Recent studies showed that also an RNA duplex synthesized by in vitro transcription can incorporate Hg 2+ ions to form uracil-Hg 2+ -uracil base pairs.…”

Section: Artificial Metal Ions-nucleic Acids Systemsmentioning

confidence: 99%

“…The stability of this Hg 2+ mediated base pair is comparable to a normal Watson-Crick base pair. [51] using different probes and mimics. These methods range from the observation of chemical shift changes, which can be done with basically any metal ion, over paramagnetic line broadening studies, to the most direct way of the detection of NOE contacts between the nucleic acid and probes like cobalt(iii)hexammine or the ammonium ion.…”

Section: Artificial Metal Ions-nucleic Acids Systemsmentioning

confidence: 99%

“…Although the development and investigation of such artificial systems is currently a popular research field, [11] only few NMR studies are known in which direct nucleic acid-metal contacts or metalinduced structural changes could be observed. [12,51] (1) (2) (1)…”

Section: Artificial Systemsmentioning

confidence: 99%

“…al were able to prove the proposed bond formation between Hg 2+ and the N(3)s of the two thymines by NMR. [51] They performed 15 N NMR experiments with DNA oligomers containing thymine-thymine mismatches in which either two labeled thymines ( Fig. 5A and C) or one labeled and one unlabeled thymine were used ( DNA strands are usually made by chemical synthesis, making it difficult to synthesize very long strands as well as high amounts thereof.…”

Section: Artificial Systemsmentioning

confidence: 99%

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Exploring Metal Ion Coordination to Nucleic Acids by NMR

Johannsen¹,

Korth²,

Schnabl³

et al. 2009

Chimia

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Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR. Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR.

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Protein Structure Design and Engineering

Berry

2011

Encyclopedia of Life Sciences

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Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-errordependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb 2+ , Cu 2+ , Hg 2+ , and UO 2 2+ . In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.

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¹⁵N−¹⁵N J-Coupling Across Hg^II: Direct Observation of Hg^II-Mediated T−T Base Pairs in a DNA Duplex

Cited by 533 publications

References 24 publications

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg²⁺ Detection

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg²⁺ Detection

Exploring Metal Ion Coordination to Nucleic Acids by NMR

Protein Structure Design and Engineering

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15N−15N J-Coupling Across HgII: Direct Observation of HgII-Mediated T−T Base Pairs in a DNA Duplex

Cited by 533 publications

References 24 publications

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg2+ Detection

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg2+ Detection

Exploring Metal Ion Coordination to Nucleic Acids by NMR

Protein Structure Design and Engineering

Contact Info

Product

Resources

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¹⁵N−¹⁵N J-Coupling Across Hg^II: Direct Observation of Hg^II-Mediated T−T Base Pairs in a DNA Duplex

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg²⁺ Detection

Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg²⁺ Detection