A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA

Hasnain, Sabeeha; Jacobson, Matthew P.; Bandyopadhyay, Pradipta

doi:10.1016/j.cplett.2013.11.029

Cited by 4 publications

(3 citation statements)

References 28 publications

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“…This approximation is in good agreement with values obtained for 20bp double-strand DNA measured by capillary electrophoresis [31]. Detailed diffusion measurements in tumor tissues [48] and extrapolation by the experimental power law n −0.67 , where n is the number of base pairs, show lower values of D (siG12D) to the range ~(0.17–1.1) × 10 −6 cm 2 /sec, yielding the a value range of 0.17 < β < 1.1 (notably, higher values of interstitial velocities associated with capillaries were observed, probably related to strong osmotic pressure or response of the IFP to blood pressure changes [10, 12])…”

Section: Model and Resultssupporting

confidence: 85%

Multistep, effective drug distribution within solid tumors

Shemi¹,

Khvalevsky²,

Gabai³

et al. 2015

Oncotarget

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The distribution of drugs within solid tumors presents a long-standing barrier for efficient cancer therapies. Tumors are highly resistant to diffusion, and the lack of blood and lymphatic flows suppresses convection. Prolonged, continuous intratumoral drug delivery from a miniature drug source offers an alternative to both systemic delivery and intratumoral injection. Presented here is a model of drug distribution from such a source, in a multistep process. At delivery onset the drug mainly affects the closest surroundings. Such ‘priming’ enables drug penetration to successive cell layers. Tumor ‘void volume’ (volume not occupied by cells) increases, facilitating lymphatic perfusion. The drug is then transported by hydraulic convection downstream along interstitial fluid pressure (IFP) gradients, away from the tumor core. After a week tumor cell death occurs throughout the entire tumor and IFP gradients are flattened. Then, the drug is transported mainly by ‘mixing’, powered by physiological bulk body movements. Steady state is achieved and the drug covers the entire tumor over several months. Supporting measurements are provided from the LODER™ system, releasing siRNA against mutated KRAS over months in pancreatic cancer in-vivo models. LODER™ was also successfully employed in a recent Phase 1/2 clinical trial with pancreatic cancer patients.

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Section: Model and Resultssupporting

confidence: 85%

Multistep, effective drug distribution within solid tumors

Shemi¹,

Khvalevsky²,

Gabai³

et al. 2015

Oncotarget

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“…In the absence of active stirrers or agitators, molecular transport relies on diffusion. For example, for a nucleic acid probe of 25 bp with a diffusion coefficient of 1.58 × 10 −11 m 2 s −1 [36] to diffuse over a distance of 100 µm, about 5 min are required; for a 1-mm diffusion distance, nearly 9 h are required. For longer probes and viscous probe solutions, these diffusion times will be significantly longer.…”

Section: Fish For Cell Analysismentioning

confidence: 99%

FISH and chips: a review of microfluidic platforms for FISH analysis

Rodriguez-Mateos

Azevedo

Almeida

et al. 2020

Med Microbiol Immunol

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Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory. Keywords Microfluidics-assisted FISH • µFISH • Microfluidics • Lab-on-a-Chip (LOC) • Fluorescence in situ hybridization (FISH) Edited by Volkhard A. J. Kempf.

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“…Diffusion has always been a subject of interest due to its wide applicability in physics, chemistry and biology [1][2][3][4][5] . The diffusion of molecules can be under the influence of concentration gradient or because of thermal motion of the molecules.…”

Section: Introductionmentioning

confidence: 99%

A memory-based random walk model to understand diffusion in crowded heterogeneous environment

Hasnain

Harbola

Bandyopadhyay

2018

Int. J. Mod. Phys. B

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We study memory based random walk models to understand diffusive motion in crowded heterogeneous environment. The models considered are non-Markovian as the current move of the random walk models is determined by randomly selecting a move from history. At each step, particle can take right, left or stay moves which is correlated with the randomly selected past step. There is a perfect stay-stay correlation which ensures that the particle does not move if the randomly selected past step is a stay move. The arXiv:1712.04151v1 [cond-mat.stat-mech]

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A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA

Cited by 4 publications

References 28 publications

Multistep, effective drug distribution within solid tumors

Multistep, effective drug distribution within solid tumors

FISH and chips: a review of microfluidic platforms for FISH analysis

A memory-based random walk model to understand diffusion in crowded heterogeneous environment

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