Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation

Saha, Sonali; Chakraborty, Kasturi; Krishnan, Yamuna

doi:10.1039/c2cc16347k

Cited by 46 publications

(39 citation statements)

References 30 publications

(5 reference statements)

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“…Parallel poly-A duplexes have been studied in terms of biophysical properties, 36, 37 structure, 32,33,38,39 and analytical applications. 35,[40][41][42] Most previous work on used pure adenine homopolymers. In our system, however, the poly-A DNA is only a fraction of the whole sequence.…”

Section: Resultsmentioning

confidence: 99%

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Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Huang

Liu

2016

Langmuir

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DNA-functionalized gold nanoparticles (AuNPs) have been extensively used in sensing, drug delivery, and materials science. A key step is to attach DNA to AuNPs forming a stable and functional conjugate. While the traditional salt-aging method takes a full day or longer, a recent low-pH method allows DNA conjugation in a few minutes. The effect of low pH was attributed to protonation of adenine (A) and cytosine (C), resulting in an overall lower negative charge density on DNA. In this work, the effect of DNA conformation at low pH is studied. Using circular dichroism (CD) spectroscopy, parallel poly-A duplex (A-motif) is detected when a poly-A segment is linked to a random DNA, a design typically used for DNA conjugation. A DNA staining dye, thiazole orange, is identified for detecting such A-motifs. The A-motif structure is ideal for DNA conjugation since it exposes the thiol group for directly reacting with gold surface while minimizing non-specific DNA base adsorption. For non-thiolated DNA, the optimal procedure is to incubate DNA and AuNPs followed by lowering the pH. The i-motif formed by poly-C DNA at low pH is less favorable for the conjugation reaction due to its unique way of folding. The stability of poly-A and poly-G DNA in low pH is examined. An excellent stability of poly-A DNA is confirmed, while poly-G has lower stability. This study provides new fundamental insights into a practically useful technique of conjugating DNA to AuNPs.3

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Section: Resultsmentioning

confidence: 99%

“…For example, poly-A DNA can form the AH + -H + A base pair by a hydrogen bond between the N7 in one adenosine and the exocyclic amino group in another ( Figure 1C). 33,35 The consequence is the formation of a parallel poly-A duplex (i.e. A-motif).…”

Section: Resultsmentioning

confidence: 99%

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Huang

Liu

2016

Langmuir

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“…Thus, building up new simple and effective strategies for pH sensing is highly valuable. To date, kinds of nano-scale materials have been reported for pH sensing by taking advantage of their unique structural and photophysical features, such as quantum dots (QDs) [23][24][25], modified nanoparticles [26][27][28] and metal NCs [29,30]. During recent years, developing metal NCs have been becoming increasingly widespread for pH sensing due to their attractive features such as low toxicity, ultra-small hydrodynamic diameters, and good biocompatibility [29,30].…”

Section: Introductionmentioning

confidence: 99%

Glutathione-stabilized Cu nanoclusters as fluorescent probes for sensing pH and vitamin B1

Luo

Miao

Yang

2015

Talanta

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“…In this regard, various metal nanoparticles based colorimetric pH sensors have been reported, including modification of gold or silver nanoparticles with DNA, 8 protein antigens, 9 and polymers. 10 Although several nanomaterials have been designed toward this end, most of these materials involve multistep and very sophisticated synthetic procedures.…”

Section: Introductionmentioning

confidence: 99%

Ionic liquid-based fluorescein colorimetric pH nanosensors

et al. 2013

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A novel pH sensitive, colorimetric ionic liquid nanosensor based on phosphonium salts of fluorescein is reported. Herein, fluorescein salts of various stoichiometries were synthesized by use of a trihexyltetradecylphosphonium cation [TTP]+ in combination with dianionic [FL]2− and monoanionic [FL]− fluorescein. Nanomaterials derived from these two compounds yielded contrasting colorimetric responses in neutral and acidic environments. Variations in fluorescence spectra as a function of pH were also observed. Examination of TEM and DLS data revealed significant expansion in the diameter of [TTP]2[FL] nanodroplets in acidic environments of variable pHs. A similar trend was also observed for [TTP][FL] nanoparticles. The pH dependent colorimetric and other optical properties of these nanomaterials are attributed to alterations in molecular orientations and stacking as suggested by measuring the absorption, fluorescence, and zeta potential. Since the pH is an important indicator for many diseases, including cancer, these nanosensors are considered to be potential candidates for biomedical applications.

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Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation

Abstract: A colorimetric pH sensor has been developed based on GNP aggregation mediated by A-motif formation under acidic conditions. The pH response of the sensor can be tuned in the range of pH 2-5.5 by changing the length and the sequence of the A-motif forming poly dA tracts.

Cited by 46 publications

References 30 publications

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Glutathione-stabilized Cu nanoclusters as fluorescent probes for sensing pH and vitamin B1

Ionic liquid-based fluorescein colorimetric pH nanosensors

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