Demonstration of pH-controlled DNA–surfactant manipulation for biomolecules

Li, Na; Liao, Zijuan; He, Shupeng; Chen, X.; Huang, Shenhao; Wang, Yanwei; Yang, Guangcan

doi:10.1039/d1ra01420j

Cited by 6 publications

(9 citation statements)

References 37 publications

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“…49 Based on these values, EP would dominate the movement, resulting in an effective movement towards the positive electrode, as was observed in our experiments. At this pH, as the 1 mM surfactant concentration is close to the CMC of the surfactant in non-ionic state, 41 some micelles are expected to get adsorbed at the oil droplet as well as the PDMS. This factor can further increase the effect of the interacting ions such as Cl − , OH − and Na + with the monomers.…”

Section: Resultsmentioning

confidence: 98%

pH-Tunable electrokinetic movement of droplets

Rashidi

Benneker

2023

Soft Matter

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Section: Resultsmentioning

confidence: 98%

pH-Tunable electrokinetic movement of droplets

Rashidi

Benneker

2023

Soft Matter

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“…In a previous mechanical measurement of DNA–lysozyme complexes in optical tweezers [ 1 ], they found that the persistence length of DNA–lysozyme complexes exhibits a nonmonotonic behavior as a function of the protein concentration. We have studied DNA complexes at various ionic and solution conditions in the past [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction

2022

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The interaction between DNA and proteins is fundamentally important not only for basic research in biology, but also for potential applications in nanotechnology. In the present study, the complexes formed by λ DNA and lysozyme in a dilute aqueous solution have been investigated using magnetic tweezers (MT), dynamic light scattering (DLS), and atomic force microscopy (AFM). We found that lysozyme induced DNA charge inversion by measuring its electrophoretic mobility by DLS. Lysozyme is very effective at neutralizing the positive charge of DNA, and its critical charge ration to induce charge inversion in solution is only 2.26. We infer that the high efficiency of charge neutralization is due to the highly positively charged (+8 e) and compact structure of lysozyme. When increasing the concentration of lysozymes from 6 ng·µL−1 to 70 ng·µL−1, DNA mobility (at fixed concentration of 2 ng·µL−1) increases from −2.8 to 1.5 (in unit of 10−4 cm2·V−1·S), implying that the effective charge of DNA switches its sign from negative to positive in the process. The corresponding condensing force increased from 0 pN to its maximal value of about 10.7 pN at concentrations of lysozyme at 25 ng·µL−1, then decreases gradually to 3.8 pN at 200 ng·µL−1. The maximal condensing force occurs at the complete DNA charge neutralization point. The corresponding morphology of DNA–lysozyme complex changes from loosely extensible chains to compact globule, and finally to less compact flower-like structure due to the change of attached lysozyme particles as observed by AFM.

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“…[1][2][3][4][5][6][7][8] For example, nucleic acids could kink with special protein residues and ions to perform various mechanical properties and regulate their elasticity of themselves in protein recognition. Thus, the structural elasticities are important for the nucleic acids, which are affected by many factors, such as the ionic DOI: 10.1002/adts.202200534 environments, [9][10][11][12][13] temperature, [14][15][16] and sequence orders. [17][18][19][20][21] It is not surprising that many studies have been devoted to the investigation of nucleic acid elastic properties by molecular dynamics simulation and experimental methods.…”

Section: Introductionmentioning

confidence: 99%

“…[32][33][34] The DNA elasticities have been investigated in various environments by experiment and computer simulation. [12,20,[35][36][37][38][39][40][41][42] For example, Qiang et al investigated the sequence-dependent of DNA elasticity for three typical AA-TT, AT-TA, and general sequences. These authors concluded [32] that in the three different sequences, polymer AA-TT chains owned a larger bending persistence length than others with only two sequences.…”

Section: Introductionmentioning

confidence: 99%

“…[37] Li et al used an experiment method to test pH controlling the surface activity of the DNA to manipulate some biological functions. [12] Smith et al studied using experiment and simulation where the multivalent ions such as Mg 2+ and Co(NH 3 ) 6 3+ had opposite effects on the persistence length and stretching modulus compared with monovalent ions for ds-DNA and dsRNA. [42] Contrary to the monovalent ions, the results showed that the multivalent ions caused a decrease in the persistence length and an increase in the stretch modulus.…”

Section: Introductionmentioning

confidence: 99%

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Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics

Zhang

Yan

Huang

et al. 2022

Advcd Theory and Sims

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Nucleic acids play essential roles in some biological processes and nanotechnology. Understanding their structural elasticity is very important for biological functions. Differences in structural elasticity of RNA and DNA duplexes are investigated by all‐atom molecular dynamics in this work. Two models double‐strand (ds) B‐DNA and A‐RNA short sequences are used. For two typical sequences, bending persistence length, stretch, and twist modulus are analyzed and compared in detail. These results demonstrate that dsDNA has a smaller bending persistence length value than dsRNA, however, the former has about 2.6 times stretch modulus than the latter one and the twist modulus in the former is smaller than the latter. Furthermore, the microstructural parameter analysis indicates that the inclination angle of a single base pair and the dihedral angle between two bases in a base pair, as well as the slide between adjacent base pairs, influences the structural elasticities of these two types of nucleic acids. Results also show that the dsDNA has a positive stretch‐twist coupling parameter while the dsRNA has a negative stretch‐twist coupling parameter. Results offer research comprehensive comparing and understanding about structural elasticity of RNA and DNA and provide novel perspectives for grasping nucleic acids' elastic properties.

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Demonstration of pH-controlled DNA–surfactant manipulation for biomolecules

Abstract: The cyclic process of the DNA extension–time curve measured by magnetic tweezers in releasing and stretching processes with different concentrations of DDAO.

Cited by 6 publications

References 37 publications

pH-Tunable electrokinetic movement of droplets

pH-Tunable electrokinetic movement of droplets

DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction

Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics

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