DNA mechanocapsules: Force responsive tetrahedral DNA nanostructures with modular cargo delivery for targeting mechanical phenotypes of diseases Open Access

Abstract

The mechanical dysregulation of cells is associated with a number of disease states, that spans from fibrosis to tumorigenesis. Hence, it is highly desirable to develop strategies to deliver drugs based on the “mechanical phenotype” of a cell. To achieve this goal, we designed and characterized DNA mechanocapsules (DMC) comprised of DNA tetrahedrons that are force responsive. Modeling showed the trajectory of force-induced DMC rupture and predicted how applied force spatial position and orientation tunes the force-response threshold. DMCs functionalized with adhesion ligands mechanically denature in vitro as a result of cell receptor forces. DMCs were designed to encapsulate macromolecular cargos such as dextran and oligonucleotide drugs with minimal cargo leakage and high nuclease resistance. Force-induced release and uptake of DMC cargo was validated by flow cytometry. Finally, we demonstrate force-induced mRNA knockdown of HIF1α in a manner that is dependent on the magnitude of cellular traction forces. These results show that DMCs can be effectively used to target biophysical phenotypes which may find useful applications in immunology and cancer biology. 

Table of Contents

CHAPTER 1                  MECHANICS OF BIOLOGICAL SYSTEMS     1

1.1 Mechanobiology of organisms across scales      2

1.1.1 Mechanical processes underly physiological and pathological process 2

1.1.2 Mechanobiology at a cellular scale          5

1.1.3 molecular underpinnings of mechanical interactions     7

1.1.4 Integrins as mechanosensors         11

1.2 Methods to study cellular forces         13

1.2.1 Force measurements on pliable substrates      13

1.2.2 Molecular tension fluorescence microscopy       15

1.3 Mechanical markers for medical applications      18

1.3.1 Clinical importance of mechanobiology         18

1.3.2 Leveraging mechanical cues         19

1.4 Developing mechanotargeting systems        21

1.4.1 Gap in the field                 21

1.4.2 DNA nanocages            22

1.5 Aims and Scope of the dissertation          24

References              27

CHAPTER 2                 DESIGN AND IN SILICO MODELING OF DMCs  40

2.3.1 ab initio DNA mechanocapsule designs       43

2.3.2 oxDNA rupture force estimation          46

2.3.3 Design force non-responsive DMC          48

2.3.4 Rupture dynamics with varying force orientations    50

2.3.5 DMC cargo leakage under force           55

CHAPTER 3             FUNCTIONAL VALIDATION OF DMCS      71

3.3.1 Synthesis of DMCs           74

3.3.2 Surface characterization            75

3.3.3 DMC response to cellular forces         79

3.3.4 Force selective DMC rupture           81

CHAPTER 4             FORCE INDUCED DRUG DELIVERY FROM DMCS  102

4.3.1 Small moelcule delivery from DMCs       106

4.3.2 Macromoelcular encapsulation inside DMCs     110

4.3.3 Macromoelcular encapsulation inside DMCs     113

4.3.4 DMCs for force-responsive rna knockdown.    116

CHAPTER 5                SUMMARY AND OUTLOOK         147

5.2.1 DMCs for precision biophysical targeting in vivo    149

5.2.2 DMCs as durable force sensors         150

5.2.3 DMCs for high throughput mechanotagging      151

5.4.1 Magnitude of LFA-1/ICAM-1 forces fine-tune TCR-triggered T cell activation 155

5.4.2 DNA origami tension sensors (DOTS) to study T-cell receptor mechanics at fluid interfaces             157

5.4.3 Tension-activated cell tagging (TaCT) for mechanocytometry    159

5.4.4 Cell adhesion receptors detect the unfolding pathway of their ligands 162

5.4.5 Loading rate estimation with DNA force probes    163

About this Dissertation

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School	Laney Graduate School
Department	Chemistry
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Chemistry, Organic Chemistry, Molecular Chemistry, Biochemistry
Keyword	Mechanobiology
Committee Chair / Thesis Advisor	Khalid Salaita, Emory University
Committee Members	David Lynn, Emory University Yonggang Ke, Emory University

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	DNA mechanocapsules: Force responsive tetrahedral DNA nanostructures with modular cargo delivery for targeting mechanical phenotypes of diseases ()	2023-08-10 02:30:44 -0400	Press to Select an action Download

Supplemental Files

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	Simulation of DMC 39pN in oxDNA under forces (DMC 39 pN was subjected to forces along the z-axis and the trajectories were recorded)	2023-07-15 17:14:59 -0400	Press to Select an action Download
	Simulation of DMC 44pN in oxDNA under forces (DMC 44 pN was subjected to forces along the z-axis and the trajectories were recorded)	2023-07-15 17:15:09 -0400	Press to Select an action Download
	Simulation of DMC 27pN in oxDNA under forces (DMC 27 pN was subjected to forces along the z-axis and the trajectories were recorded)	2023-07-15 17:15:23 -0400	Press to Select an action Download
	Simulation of DMC rigid in oxDNA under forces (DMC rigid was subjected to forces along the z-axis and the trajectories were recorded)	2023-07-15 17:15:37 -0400	Press to Select an action Download