Nonmonotonous variation of <scp>DNA</scp> angular separation during asymmetric pulsed field electrophoresis

Nazemifard, Neda; Bhattacharjee, Subir; Masliyah, Jacob H.; Harrison, David

doi:10.1002/elps.201300152

Cited by 4 publications

(5 citation statements)

References 49 publications

(80 reference statements)

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“…Without trapping, the motion of DNA in APFE should follow a ratchet model, 6,23,24 wherein a DNA stream or plug migrates vertically while being deected at a certain angle (Fig. 2a-c).…”

Section: Macroscopic Behaviors Of T4 Dna Trappingmentioning

confidence: 99%

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

Zhou

Sheng

Harrison

2014

Analyst

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We investigate the trapping mechanism of individual DNA molecules in ordered nanoporous structures generated by crystalline particle arrays. Two requisites for trapping are revealed by the dynamics of single trapped DNA, fully-stretched U/J shapes and hernia formation. The experimental results show there is a stronger possibility for hernias to lead the reorientation upon switching directions of the voltage at high field strengths, where trapping occurs. Fully stretched DNA has longer unhooking times than expected by a classic rope-on-pulley model. We propose a dielectrophoretic (DEP) force reduces the mobility of segments at the apex of the U or J, where field gradients are highest, based on simulations and observations of the trapping force dependence on field strength. A modified model for unhooking time is obtained after the DEP force is introduced. The new model explains the unhooking time data by predicting an infinite trapping time when the ratio of arm length differences (of the U or J) to molecule length Δx/L < β, where β is a DEP parameter that is found to strongly increase with electric field. The DNA polarizability calculated with the DEP model and experimental value of β is of the same magnitude of reported value. The results indicate the tension at the apex of U/J shape DNA is the primary reason for DNA trapping during pulsed field separation, instead of hernias.

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“…Without trapping, the motion of DNA in APFE should follow a ratchet model, 6,23,24 wherein a DNA stream or plug migrates vertically while being deected at a certain angle (Fig. 2a-c).…”

Section: Macroscopic Behaviors Of T4 Dna Trappingmentioning

confidence: 99%

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

Zhou

Sheng

Harrison

2014

Analyst

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“…Variations on this theme include pulsed field electrophoresis through arrays of micropillers 65 or nanoparticles (Fig. 2d) 66 , tilted Brownian ratcheting 67, 68 , and deterministic lateral displacement 69 . In general, these methods are limited to large DNA molecules (10’s to 100’s of kb) with limited demonstrated integration with single molecule detection.…”

Section: Assessment Modalitiesmentioning

confidence: 99%

“…Pulsed electric fields across a micropillar array are used to continuously separate DNA fragments sized 20 kbp to 166 kbp (picture reprinted with permission from ref. 66 ).…”

Section: Figurementioning

confidence: 99%

Analysis of single nucleic acid molecules in micro- and nano-fluidics

2016

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Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano- fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano- fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano- structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

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“…TIRF can provide information on bitumen distribution and the bitumen−clay interaction in tailings in real time, showing the effect of change in the temperature, pressure, flocculants, and pH. 34,35 First, we present the fluorescence excitation and emission spectra and show that it is possible to observe the bitumen− clay and bitumen−water interfaces using confocal epifluorescence microscopy. Then, we show the distribution of bitumen in MFT using TIRF images.…”

Section: Introductionmentioning

confidence: 99%

“…The illumination depth in TIRF can be made as small as 100 nm to eliminate the background noise, enabling imaging of detailed features. TIRF can provide information on bitumen distribution and the bitumen–clay interaction in tailings in real time, showing the effect of change in the temperature, pressure, flocculants, and pH. , …”

Section: Introductionmentioning

confidence: 99%

Total Internal Reflection Fluorescence Microscopy To Investigate the Distribution of Residual Bitumen in Oil Sands Tailings

Shende¹,

Pendharker²,

Jacob

et al. 2016

Energy Fuels

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A major waste byproduct of oil sands in situ extraction is oil sands tailings, which are a mixture of water, clay, and residual bitumen. These tailings represent a huge ecological footprint in the form of tailings ponds, which not only render large land areas unusable but also prevent reuse of water. The slow dewatering of the tailings ponds poses a major challenge to the industry. The presence of complex inorganic−organic bitumen−clay mixtures in these tailings contributes to this problem. Hence, understanding the nature of the bitumen−clay association and the effect of bitumen on clay particle−particle interactions is important for the development of more effective chemicals or processes to accelerate particle aggregation and sedimentation during dewatering. Previous studies that investigate these interactions used techniques that are sensitive only toward inorganic clay but not sensitive towards organic bitumen. Here, we use a high-resolution total internal reflection fluorescence (TIRF) microscopy to help identify the accurate location and distribution of bitumen in mature fine tailings (MFT) samples. We report the first adaptation of TIRF beyond cell biology for visualization of bitumen and its interaction with clay. The high signal-to-noise ratio of TIRF microscopy and a high contrast between the clay and residual bitumen provide images that reveal a wealth of information about the bitumen coverage on clay as well as clay−clay aggregates and how the bitumen positions itself within these aggregates. These images confirm the presence of hydrophobic fine clay agglomerates along with the hydrophilic clay particles in MFT. It is also observed that bitumen coats clay particles, bridges clay agglomerates, and is mostly absent as free bitumen in the bulk of the MFT sample. Our work paves the way for the use of nanophotonic tools in oil sands imaging and provides strategic suggestions for the development of better methods for clay sedimentation and bitumen recovery.

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Nonmonotonous variation of DNA angular separation during asymmetric pulsed field electrophoresis

Cited by 4 publications

References 49 publications

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

Analysis of single nucleic acid molecules in micro- and nano-fluidics

Total Internal Reflection Fluorescence Microscopy To Investigate the Distribution of Residual Bitumen in Oil Sands Tailings

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