DNA release dynamics from reducible polyplexes by atomic force microscopy

Polycondensed Peptide-Based Polymers for Targeted Delivery of Anti-Angiogenic siRNA to Treat Endometriosis

Endometriosis (EM) is a prevalent gynecological disease characterized by the abnormal growth of tissue similar to the endometrium outside of the uterus. This condition is accompanied by the development of new blood vessels in endometriotic lesions. While surgical intervention is effective in removing endometriotic lesions, some patients require multiple surgeries. Therefore, finding non-surgical treatments for EM is of great interest. One of the promising approaches is anti-angiogenic therapy using siRNA-therapeutics to target the expression of the VEGFA gene. Peptide-based polymers have shown promise as siRNA delivery systems due to their biocompatibility and ease of modification. We conducted a study to evaluate the effectiveness of the R6p-cRGD peptide carrier as a non-viral vehicle for delivering siRNA to endothelial cells in vitro and endometrial implants in vivo. We investigated the physicochemical properties of the siRNA-complexes, assessed cellular toxicity, and examined the efficiency of GFP and VEGFA genes silencing. Furthermore, we tested the anti-angiogenic effects of these complexes in cellular and animal models. The transfection with siRNA complexes led to a significant increase in VEGFA gene knockdown efficiency and a decrease in the migration of endothelial cells. For the animal model, we induced endometriosis in rats by transplanting endometrial tissue subcutaneously. We evaluated the efficiency of anti-angiogenic therapy for EM in vivo using anti-VEGF siRNA/R6p-RGD complexes. During this assessment, we measured the volume of the implants, analyzed VEGFA gene expression, and conducted CD34 immunohistochemical staining. The results showed a significant decrease in the growth of endometriotic implants and in VEGFA gene expression. Overall, our findings demonstrate the potential of the R6p-cRGD peptide carrier as a delivery system for anti-angiogenic therapy of EM.

A review of the tortuous path of nonviral gene delivery and recent progress

Gene therapy encompasses the transfer of exogenous genetic materials into the patient's target cells to treat or prevent diseases. Nevertheless, the transfer of genetic material into desired cells is challenging and often requires specialized tools or delivery systems. For the past 40 years, scientists are mainly pursuing various viruses as gene delivery vectors, and the overall progress has been slow and far from the expectation. As an alternative, nonviral vectors have gained substantial attention due to their several advantages, including superior safety profile, enhanced payload capacity, and stealth abilities. Since nonviral vectors encounter multiple extra- and intra-cellular barriers limiting the transfer of genetic payload into the target cell nucleus, we have discussed these barriers in detail for this review. A direct approach, utilizing physical methods like electroporation, sonoporation, gene gun, eliminate the requirement for a specific carrier for gene delivery. In contrast, chemical methods of gene transfer exploit natural or synthetic compounds as carriers to increase cellular targeting and gene therapy effectiveness. We have also emphasized the recent advancements aimed at enhancing the current nonviral approaches. Therefore, in this review, we have focused on discussing the current evolving state of nonviral gene delivery systems and their future perspectives.

Effect of Double Substitution in Cationic Chitosan Derivatives on DNA Transfection Efficiency

Recently, much effort has been expended on the development of non-viral gene delivery systems based on polyplexes of nucleic acids with various cationic polymers. Natural polysaccharide derivatives are promising carriers due to their low toxicity. In this work, chitosan was chemically modified by a reaction with 4-formyl-n,n,n-trimethylanilinium iodide and pyridoxal hydrochloride and subsequent reduction of the imine bond with NaBH₄. This reaction yielded three novel derivatives, n-[4-(n’,n’,n’-trimethylammonium)benzyl]chitosan chloride (TMAB-CS), n-[(3-hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridine)methyl]chitosan chloride (Pyr-CS), and n-[4-(n’,n’,n’’-trimethylammonium)benzyl]-n-[(3-hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridine)methyl]chitosan chloride (PyrTMAB-CS). Their structures and degrees of substitution were established by ¹H NMR spectroscopy as DS₁ = 0.22 for TMAB-CS, DS₂ = 0.28 for Pyr-CS, and DS₁ = 0.21, DS₂ = 0.22 for PyrTMAB-CS. Dynamic light scattering measurements revealed that the new polymers formed stable polyplexes with plasmid DNA encoding the green fluorescent protein (pEGFP-N3) and that the particles had the smallest size (110–165 nm) when the polymer:DNA mass ratio was higher than 5:1. Transfection experiments carried out in the HEK293 cell line using the polymer:DNA polyplexes demonstrated that Pyr-CS was a rather poor transfection agent at polymer:DNA mass ratios less than 10:1, but it was still more effective than the TMAB-CS and PyrTMAB-CS derivatives that contained a quaternary ammonium group. By contrast, TMAB-CS and PyrTMAB-CS were substantially more effective than Pyr-CS at higher polymer:DNA mass ratios and showed a maximum efficiency at 200:1 (50%–70% transfected cells). Overall, the results show the possibility of combining substituent effects in a single carrier, thereby increasing its efficacy.

New Insights into the Interactions of a DNA Oligonucleotide with mPEGylated-PAMAM by Circular Dichroism and Solution NMR

Dendrimers are well-defined, highly branched, synthetic three-dimensional molecules with a large number of reactive end groups. PAMAM dendrimers form stable complexes with DNA chemistries and constitute an important class of nonviral, cationic vectors in gene delivery. The aim of this study is to examine the interactions of a 12 bp DNA oligonucletide with PAMAM-G2 and mPEG- b-PAMAM-G3 having eight surface amine groups under physiological conditions, using constant DNA concentration but varying dendrimer concentration. 1D ³¹P NMR, 2D NOESY, and CD spectroscopic methods were employed to investigate the interactions between the dendrimer and the DNA. The CD experiments carried out with a constant DNA concentration of 25 μM and dendrimer concentrations from 0 to 100 μM indicated minimal change to the chirality of the DNA for both types of dendrimers. While the PAMAM-G2 dendrimer caused aggregation of the majority of the DNA, the 2D NMR data of the DNA with an mPEG- b-PAMAM-G3 dendrimer indicated general broadening of the 1D ³¹P peaks from the DNA phosphates, a small number of ¹H chemical shift perturbations (CSPs), and reduction of specific ¹H-¹H NOE intensities. These data suggest there is minimal structural alteration of the DNA in the complex and indicate preferential binding of the dendrimer to the central AATT region of the DNA sequence. The results herein are the first such results demonstrating a soluble DNA complex with the mPEG- b-PAMAM-G3 dendrimer analyzed by multidimensional NMR.

In Situ AFM Analysis Investigating Disassembly of DNA Nanoparticles and Nanofilms

Synthetic vector-based gene delivery continues to gain strength as viable alternatives to viral vectors due to safety and other concerns. DNA release dynamics is key to the understanding and control of gene delivery from nanosystems. Here we describe atomic force microscope (AFM) application to the understanding of DNA release dynamics from bioreducible polycation-based nanosystems. The two nanosystems are polyplex nanoparticles and layer-by-layer (LbL) films.

Stimuli-Responsive Gold Nanoparticles for Cancer Diagnosis and Therapy

An emerging concept is that cancers strongly depend on both internal and external signals for growth and invasion. In this review, we will discuss pathological and physical changes in the tumor microenvironment and how these changes can be exploited to design gold nanoparticles for cancer diagnosis and therapy. These intrinsic changes include extracellular and intracellular pH, extracellular matrix enzymes, and glutathione concentration. External stimuli include the application of laser, ultrasound and X-ray. The biology behind these changes and the chemistry behind the responding mechanisms to these changes are reviewed. Examples of recent in vitro and in vivo studies are also presented, and the clinical implications of these findings are discussed.

Stimuli-Responsive Gold Nanoparticles for Cancer Diagnosis and Therapy

An emerging concept is that cancers strongly depend on both internal and external signals for growth and invasion. In this review, we will discuss pathological and physical changes in the tumor microenvironment and how these changes can be exploited to design gold nanoparticles for cancer diagnosis and therapy. These intrinsic changes include extracellular and intracellular pH, extracellular matrix enzymes, and glutathione concentration. External stimuli include the application of laser, ultrasound and X-ray. The biology behind these changes and the chemistry behind the responding mechanisms to these changes are reviewed. Examples of recent in vitro and in vivo studies are also presented, and the clinical implications of these findings are discussed.

Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release

A combination of solution NMR, dynamic light scattering (DLS), and fluorescence quenching assays were employed to obtain insights into the dynamics and structural features of a polyplex system consisting of HIV-1 transactivation response element (TAR) and PEGylated generation 5 poly(amidoamine) dendrimer (G5-PEG). NMR chemical shift mapping and (13)C spin relaxation based dynamics measurements depict the polyplex system as a highly dynamic assembly where the RNA, with its local structure and dynamics preserved, rapidly exchanges ( Collapse

Key Words

• therapeutic rna delivery
• pamam
• pegylation
• tar
• dls
• nmr spin relaxation

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MESH Headings

• Dendrimers/chemistry
• HIV-1/chemistry
• Magnetic Resonance Spectroscopy/methods
• Polyamines/chemistry
• Polyethylene Glycols/chemistry
• RNA/chemistry
• Response Elements/genetics
• Transfection/methods

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Grants

• R01 AI066975 NIAID NIH HHS
• P50 GM103297 NIGMS NIH HHS
• R01 AI087463-01 NIAID NIH HHS
• R01 EB005028 NIBIB NIH HHS
• R01EB005028 NIBIB NIH HHS
• R01 GM089846 NIGMS NIH HHS

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Affiliation(s)

Anisha Shakya Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
Casey A. Dougherty Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
Yi Xue Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
Hashim M. Al-Hashimi Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
Mark M. Banaszak Holl Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA

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Complexation and release of DNA in polyplexes formed with reducible linear poly(β-amino esters)

Designing nanocarriers for gene delivery is a multidisciplinary challenge that involves not only DNA condensation with biocompatible polymers, but also DNA-release processes. Once the genetic material is introduced into the cell, the rupture of degradable bonds permits the unpacking and release of the load. In this work, a dual-degradable polycation - composed by a linear poly(β-amino ester) chain in which ester and disulfide bonds coexist - has been used to condense a DNA plasmid. The goal was to reinforce the spontaneous hydrolysis of the ester groups with the intracellular break-up of the disulfide bonds, since these reducible bonds are degraded in the reductive intracellular environment. For a comparative study, two poly(β-amino ester) molecules differing only in the presence (or absence) of some SS bonds have been tested. DNA condensation, physico-chemical characterization of the polyplexes formed, and degradation studies have been carried out at pH 5 and pH 7. The acidic conditions gave the best nanoparticles, due to a better solubilization of both polymers and to a higher stability of the ester bonds. Despite the synthesis and storage of polyplexes were much more appropriate at pH 5, transfection efficiency in HeLa cells was similar irrespective the original pH used. Only in those polyplexes formed at low polymer:DNA ratios (i.e. 5 and 10 (w/w)) was transfection more effective when the plasmid was condensed at an acidic pH. With regard to the DNA-release efficiency in the intracellular medium, degradation of the polymers was practically governed by the rapid hydrolysis of the ester groups, this spontaneous and rapid process masking, unfortunately, any potential contribution associated with the breakup of the disulfide bonds.

Surfactant-triggered disassembly of electrostatic complexes probed at optical and quartz crystal microbalance length scales

A critical advantage of electrostatic assemblies over covalent and crystalline bound materials is that associated structures can be disassembled into their original constituents. Nanoscale devices designed for the controlled release of functional molecules already exploit this property. To bring some insight into the mechanisms of disassembly and release, we study the disruption of molecular electrostatics-based interactions via competitive binding with ionic surfactants. To this aim, free-standing micrometer-size wires were synthesized using oppositely charged poly(diallyldimethylammonium chloride) and poly(acrylic acid) coated iron oxide nanoparticles. The disassembly is induced by the addition of sodium dodecyl sulfates that complex preferentially the positive polymers. The process is investigated at two different length scales: the length scale of the particles (10 nm) through the quartz crystal microbalance technique and that of the wires (>1 μm) via optical microscopy. Upon surfactant addition, the disassembly is initiated at the surface of the wires by the release of nanoparticles and by the swelling of the structure. In a second step, erosion involving larger pieces takes over and culminates in the complete dissolution of the wires, confirming the hypothesis of a surface-type swelling and erosion process.

Endosomolytic reducible polymeric electrolytes for cytosolic protein delivery

Despite the numerous vital functions of proteins in the cytosolic compartment, less attention has been paid to the delivery of protein drugs to the cytosol than to the plasma membrane. To address this issue and effectively deliver charged proteins into the cytoplasm, we used endosomolytic, thiol-triggered degradable polyelectrolytes as carriers. The cationic, reducible polyelectrolyte RPC-bPEI(0.8 kDa)2 was synthesized by the oxidative polymerization of thiolated branched polyethyleneimine (bPEI). The polymer was converted to the anionic, reducible polyelectrolyte RPA-bPEI(0.8 kDa)2 by introducing carboxylic acids. The two reducible polyelectrolytes (RPC-bPEI(0.8 kDa)2 and RPA-bPEI(0.8 kDa)2) were complexed with counter-charged model proteins (bovine serum albumin (BSA) and lysozyme (LYZ)), forming polyelectrolyte/protein complexes of less than 200 nm in size at weight ratios (WR) of ≥1. The resultant complexes maintained a proton buffering capacity nearly equivalent to that of the polyelectrolytes in the absence of protein complexation and were cytocompatible with MCF7 human breast carcinoma cells. Under cytosol-mimicking thiol-rich conditions, RPC-bPEI(0.8 kDa)2/BSA and RPA-bPEI(0.8 kDa)2/LYZ complexes increased significantly in size and released the loaded protein, unlike the protein complexes with nonreducible polyelectrolytes (bPEI(25 kDa) and bPEI(25 kDa)COOH). The polyelectrolyte/protein complexes showed cellular uptake similar to that of the corresponding proteins alone, but the former allowed more protein to escape into the cytosol from endolysosomes than the latter as a result of the endosomolytic function of the polyelectrolytes. In addition, the proteins in the polyelectrolyte/protein complexes kept their intrinsic secondary structures. In conclusion, the results show the potential of the designed endosomolytic, reducible polyelectrolytes for the delivery of proteins to the cytosol.

In situ AFM analysis investigating disassembly of DNA nanoparticles and nano-films

Synthetic vector-based gene delivery systems continue to gain strength as viable alternatives to viral vectors due to safety and other concerns. DNA release dynamics is key to the understanding and control of gene delivery from nano-systems. Here we describe atomic force microscope application to the understanding of DNA release dynamics from bioreducible polycation-based nano-systems. The two nano-systems are polyplex nanoparticles and layer-by-layer films.

Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release

The transfer of genetic material into cells using nonviral vectors offers unique potential for therapeutics; however, the efficacy of delivery depends upon a poorly understood, multistep pathway, limiting the prospects for successful gene delivery. Mechanistic insight into DNA association and release has been hampered by a lack of atomic resolution structural and dynamic information for DNA-polymer complexes (polyplexes). Here, we report a dendrimer-based polyplex system containing poly(ethyleneglycol) (PEG) arms that is suitable for atomic-level characterization by solution NMR spectroscopy. NMR chemical shift, line width, and proton transverse relaxation rate measurements reveal that free and dendrimer-bound polyplex DNA exchange rapidly relative to the NMR time scale (<millisecond). The dendrimers retain a high degree of mobility in the polyplex, whereas the DNA shows restrained mobility, suggesting that the polyplex is a highly dynamic complex with a rapidly exchanging dendrimer atmosphere around a more rigid DNA framework.

Nanoparticles change the ordering pattern of n-carboxylic acids into nanorods on HOPG

This paper describes the formation of organic nanorods induced by monolayer-protected inorganic nanoparticles. Alkanes and alkane derivatives, such as n-carboxylic acids, self-assemble on highly oriented pyrolytic graphite (HOPG) into a persistent molecular packing structure that is dictated by the epitaxial interaction between the carbon chain plane and the HOPG basal plane. Carboxylic acids form 2-D crystalline layers consisting of nanostripe domains whose periodicity is one or two times the molecular chain length. However, when the molecular ordering occurs in the vicinity of a nanoparticle, this persistent HOPG-dominated nanostripe pattern is disrupted, and nanorods attached to the nanoparticles become the dominant structure. In order to understand the underlying mechanism of the nanoparticle-mediated nanorod formation, the effects of film-forming conditions, carboxylic acid chain length, nanoparticle size, and chemical composition of the nanoparticle are examined. It is determined that carboxylic acid nanorods can be induced by nanoparticles of different core materials including CdSe, CdS, and Au, as long as the protecting monolayer allows sufficient dispersion and colloidal stability of the nanoparticles in solution. A carboxylic chain length range amenable to the nanorod formation is identified, as is the relationship between the nanoparticle size and the number of nanorods per nanoparticle. This study contributes to the understanding of seed-mediated crystallization and molecular ordering. Moreover, it defines the parameters governing solution-based formation of hybrid nanostructures and nanopatterns incorporating dual functionality as defined by the inorganic nanoparticle and organic nanorod, respectively.

DNA release dynamics from bioreducible layer-by-layer films

DNA release dynamics from layer-by-layer (LbL) films is an important aspect to consider with regards to localized gene delivery systems. The rate of DNA release and the condensation state of DNA during release are of particular interest in the field of gene delivery. A hyperbranched poly(amido amine) (RHB) containing bioreducible disulfide bonds is used to form interpolyelectrolyte complexes with DNA during LbL film assembly. During film disassembly, DNA is released in physiologic conditions due to the reducing nature of the RHB. Uncondensed DNA deposited on the surface was compared to DNA condensed by RHB in polyplex form by using two types of LbL films, RHB/DNA/RHB and polyplex terminated films, RHB/DNA/polyplex. LbL films with up to three layers are used in order to facilitate high-resolution atomic force microscopy (AFM) imaging. X-ray reflectivity, ellipsometry, and Fourier transform infrared spectroscopy are also used. The film disassembly, rearrangement, and release of molecules from the surface due to thiol-disulfide exchange is conducted in reducing dithiothreitol (DTT) solutions. Salt is found to accelerate the overall rate of film disassembly. Additionally, it was found that the polyplex layer disassembles faster than the DNA layer. The predominant intermediate structure is the toroid structure for the polyplex layer and the fiber bundle structure for the DNA layer during film disassembly. This study offers a simple means to modulate DNA release from LbL films by utilizing both condensed and uncondensed DNA in different layers. The study highlights nanostructures, toroids, and bundles as dominant intermediate DNA structures during DNA release from LbL films.

Reducible DNA nanoparticles enhance in vitro gene transfer via an extracellular mechanism

We developed polylysine based DNA nanoparticles (DNA NPs) that contain disulfide linkage in the carrier and demonstrated that this reducible DNA NP enhances in vitro gene transfer via an extracellular mechanism. Polylysine was conjugated through an N-terminal cysteine to a polyethylene glycol chain (PEG) by either a disulfide bond (SS) or a thioether bond (CS), and the resulting PEG-peptide conjugates were used to compact plasmid DNA into reducible SS-DNA NPs or non-reducible CS-DNA NPs with identical physical properties. SS-DNA NPs mediated more than 10-fold higher in vitro gene transfer. Others have suggested that disulfide bonds in synthetic gene carriers undergo cleavage in the reducing environment inside the cell, allowing increased intracellular DNA release. In this study, however, both higher cellular uptake of SS-DNA NPs and inhibition of SS-DNA NP mediated in vitro gene transfer by blocking extracellular free thiols suggested an extracellular mechanism. DePEGylation of SS-DNA NPs by extracellular thiols caused aggregation which might lead to higher cellular uptake and higher transgene expression. A series of SS-DNA NPs prepared with stabilized disulfide bonds survived the extracellular environment without aggregation but lost the superior gene transfer ability, indicating that, in our system, intracellular mechanisms are not involved. These results provided further insight into the mechanisms of in vitro gene transfer enhancement by introducing reducible linkages, contributing to the rational design of more efficient non-viral gene delivery systems.

DNA release dynamics from bioreducible poly(amido amine) polyplexes

The DNA release dynamics of bioreducible poly(amido amine) polyplexes were studied in real time by atomic force microscopy (AFM). DNA release is triggered by a depolymerization of high-molecular-weight polycations into low-molecular-weight oligocations that occurs by means of the thiol and disulfide exchange reaction mechanism. AFM images were captured in a simulated physiological reducing environment that used dithiothreitol. Distinctive stages of disassembly are common among various polyplexes that have different disulfide content, molecular weight, and polymer architecture, while the DNA release rate depends upon the disulfide content. In the first stage, polyplexes evolve from metastable structures into the more stable toroid structure upon the depolymerization. In the second stage, toroids either aggregate or fuse into larger toroids. In the last stage, DNA wormlike chains and loops are held by a central compact core. The results confirm the prospect of bioreducible poly(amido amine)s as controlled DNA delivery vectors. The study offers new physical insights into the DNA release pathway including intermediate structures that have a high degree of structural heterogeneity and disassembly induced particle growth. The study identifies disassembly induced colloidal and morphological instability as an important issue to be addressed.

Multifunctional Dendrimer-templated Antibody Presentation on Biosensor Surfaces for Improved Biomarker Detection

Dendrimers, with their well-defined globular shape and a high density of functional groups, are ideal nanoscale materials for templating sensor surfaces. This work exploits dendrimers as a versatile platform for capturing biomarkers with improved sensitivity and specificity. Synthesis, characterization, fabrication, and functional validation of the dendrimer-based assay platform are described. Bifunctional hydroxyl/thiol functionalized G4-polyamidoamine (PAMAM) dendrimer is synthesized and immobilized on to the polyethylene-glycol (PEG)-functionalized assay plate by coupling PEG-maleimide and dendrimer thiol groups. Simultaneously, part of the dendrimer thiol groups are converted to hydrazide functionalities. The resulting dendrimer-modified surface is coupled to the capture antibody in the Fc region of the oxidized antibody. This preserves the orientation flexibility of the antigen binding region (Fv) of the antibody. To validate the approach, the fabricated plates are further used as a solid phase for developing a sandwich type ELISA to detect IL-6 and IL-1β, important biomarkers for early stages of chorioamnionitis. The dendrimer-modified plate provides assays with significantly enhanced sensitivity, lower nonspecific adsorption, and a detection limit of 0.13 pg ml-1 for IL-6 luminol detection and 1.15 pg ml-1 for IL-1β TMB detection, which are significantly better than those for the traditional ELISA. The assays were validated in human serum samples from normal (non-pregnant) woman and pregnant women with pyelonephritis. The specificity and the improved sensitivity of the dendrimer-based capture strategy could have significant implications for the detection of a wide range of cytokines and biomarkers since the capture strategy could be applied to multiplex microbead assays, conductometric immunosensors and field effect biosensors.

Effect of innate glutathione levels on activity of redox-responsive gene delivery vectors

Redox-responsive polyplexes represent a promising class of non-viral gene delivery vectors. The reducible disulfide bonds in the polyplexes undergo intracellular reduction owing to the presence of high concentrations of reduced glutathione (GSH). Available evidence suggests improved transfection activity of redox-sensitive polyplexes upon artificial modulation of intracellular GSH. This study investigates the effect of innate differences in GSH concentration in a panel of human pancreatic cancer cell lines on activity of reducible polyplexes of the four major classes of nucleic acid therapeutics: plasmid DNA (pDNA), messenger RNA (mRNA), antisense oligodeoxynucleotides (AON) and siRNA. In general, reducible polyplexes of linear poly(amido amines) (PAA) show improved activity compared to non-reducible polyplexes of PAA. Results demonstrate that increased GSH levels are associated with improved transfection of mRNA polyplexes but no clear trend is observed for pDNA, AON and siRNA polyplexes.