The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength

Wang, Yanwei; Wang, Ruxia; Gao, Tianyong; Yang, Guangcan

doi:10.3390/polym10030244

Cited by 12 publications

(23 citation statements)

References 51 publications

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“…In our previous study, the ratio of the saturated electrophoretic mobility of DNA in monovalent and divalent cation solution is about 1:2, and the ratio becomes 1:4.5 for the case of monovalent versus trivalent counterions [ 28 , 29 , 30 ]. In the framework of the Manning theory, we can infer the critical charge neutralization of DNA for its compaction.…”

Section: Resultsmentioning

confidence: 99%

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

et al. 2019

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DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around −1.0 × 10−4 cm2 V−1 s−1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.

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Section: Resultsmentioning

confidence: 99%

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

et al. 2019

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“…We speculate that Manning’s theory of counterion condensation could play a role in such conditions. Since gDNA is basically a long polyanionic rod spanning up to 3.2 million bases of negative phosphate molecules, monovalent ions in the PBS buffer and already existing other di/trivalent ions present within the extracted gDNA sample could very well contribute to counterions condensation along the gDNA’s length, resulting in counterion-induced negative charge neutralization 66–68 . Besides this, natural compaction of the large gDNA strand into a denser, packed structure (resultant of counterion condensation) under in-vitro conditions and low-temperature induced strand folding during hybridization steps could likewise also contribute to lower negative potential 69,70 .…”

Section: Resultsmentioning

confidence: 99%

Gold-Hybridized Zinc Oxide Nanorods as Real-Time Low-Cost NanoBiosensors for Detection of virulent DNA signature of HPV-16 in Cervical Carcinoma

Thevendran

Foo

Haarindraprasad

et al. 2019

Sci Rep

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Detection of host integrated viral oncogenes are critical for early and point-of-care molecular diagnostics of virus-induced carcinoma. However, available diagnostic approaches are incapable of combining both cost-efficient medical diagnosis and high analytical performances. To circumvent this, we have developed an improved IDE-based nanobiosensor for biorecognition of HPV-16 infected cervical cancer cells through electrochemical impedance spectroscopy. The system is fabricated by coating gold (Au) doped zinc oxide (ZnO) nanorods interfaced with HPV-16 viral DNA bioreceptors on top of the Interdigitated Electrode (IDE) chips surface. Due to the concurrently improved sensitivity and biocompatibility of the designed nanohybrid film, Au decorated ZnO-Nanorod biosensors demonstrate exceptional detection of HPV-16 E6 oncogene, the cancer biomarker for HPV infected cervical cancers. This sensor displayed high levels of sensitivity by detecting as low as 1fM of viral E6 gene target. The sensor also exhibited a stable functional life span of more than 5 weeks, good reproducibility and high discriminatory properties against HPV-16. Sensor current responses are obtained from cultured cervical cancer cells which are close to clinical cancer samples. Hence, the developed sensor is an adaptable tool with high potential for clinical diagnosis especially useful for economically challenged countries/regions.

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“…The negative velocity regime observed in experiments [61,62] and simulations [34][35][36] corresponds to an unconventional transport picture characterized by an anionic polymer translating parallel with the electric field.…”

Section: Mobility Inversion Of Strongly Anionic Biopolymersmentioning

confidence: 84%

“…In the case of strongly charged biopolymers such as DNA translocating in the highly multivalent KCl+Spm 4+ mixture [61,62], the polarization-driven EO flows are expected to act together with the strongcoupling correlations governing the vicinity of the polymer. With the aim to investigate the outcome of this coupling, we reported in Fig.…”

Section: Mobility Inversion Of Strongly Anionic Biopolymersmentioning

confidence: 99%

Dielectric manipulation of polymer translocation dynamics in engineered membrane nanopores

Buyukdagli

2021

Preprint

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The alteration of the dielectric membrane properties by carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in surface-coated pores confining mixed electrolytes. In the giant permittivity regime of CNT-coated membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation and set an electroosmotic (EO) flow. The drag force exerted by this flow is sufficiently strong to suppress and invert the electrophoretic (EP) velocity of anionic polymers, and also to generate the mobility of neutral polymers whose speed and direction can be solely adjusted by the charge and concentration of the added multivalent ions. These features identify the dielectrically generated transport mechanism as an efficient mean to drive overall neutral or weakly charged analytes that cannot be controlled by an external voltage. We also reveal that in anionic polymer translocation, multivalent cation addition into the monovalent salt solution amplifies the electric current signal by several factors. The signal amplification is caused by the electrostatic many-body interactions replacing the monovalent polymer counterions by the multivalent cations of higher electric mobility. The strength of this elektrokinetic charge discrimination points out the potential of multivalent ions as current amplifiers capable of providing boosted resolution in nanopore-based biosensing techniques.

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The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength

Cited by 12 publications

References 51 publications

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

Gold-Hybridized Zinc Oxide Nanorods as Real-Time Low-Cost NanoBiosensors for Detection of virulent DNA signature of HPV-16 in Cervical Carcinoma

Dielectric manipulation of polymer translocation dynamics in engineered membrane nanopores

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