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Papers by Andrew Prigodich

Research paper thumbnail of Selective enhancement of nucleases by polyvalent DNA-functionalized gold nanoparticles

Journal of the American Chemical Society, Feb 1, 2011

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enh... more We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling proteinnanoparticle interactions.

Research paper thumbnail of Short Duplex Probes for Enhanced Target Hybridization

Research paper thumbnail of Polyvalent rna-nanoparticle compositions

Research paper thumbnail of Scavenger Receptors Mediate Cellular Uptake of Polyvalent Oligonucleotide-Functionalized Gold Nanoparticles

Bioconjugate Chemistry, 2010

Mammalian cells have been shown to internalize oligonucleotide-functionalized gold nanoparticles ... more Mammalian cells have been shown to internalize oligonucleotide-functionalized gold nanoparticles (DNA-Au NPs or siRNA-Au NPs) without the aid of auxiliary transfection agents and use them to initiate an antisense or RNAi response. Previous studies have shown that the dense monolayer of oligonucleotides on the nanoparticle leads to the adsorption of serum proteins and facilitates cellular uptake. Here, we show that serum proteins generally act to inhibit cellular uptake of DNA-Au NPs. We identify the pathway for DNA-Au NPs entry in HeLa cells.

Research paper thumbnail of Polyvalent DNA Nanoparticle Conjugates Stabilize Nucleic Acids

Nano Letters, 2009

Polyvalent oligonucleotide gold nanoparticle conjugates have unique fundamental properties includ... more Polyvalent oligonucleotide gold nanoparticle conjugates have unique fundamental properties including distance-dependent plasmon coupling, enhanced binding affinity, and the ability to enter cells and resist enzymatic degradation. Stability in the presence of enzymes is a key consideration for therapeutic uses; however the manner and mechanism by which such nanoparticles are able to resist enzymatic degradation is unknown. Here, we quantify the enhanced stability of polyvalent gold oligonucleotide nanoparticle conjugates with respect to enzyme-catalyzed hydrolysis of DNA and present evidence that the negatively charged surfaces of the nanoparticles and resultant high local salt concentrations are responsible for enhanced stability.

Research paper thumbnail of Nano-Flares:  Probes for Transfection and mRNA Detection in Living Cells

Journal of the American Chemical Society, 2007

We demonstrate that novel oligonucleotide-modified gold nanoparticle probes hybridized to fluorop... more We demonstrate that novel oligonucleotide-modified gold nanoparticle probes hybridized to fluorophore-labeled complements can be used as both transfection agents and cellular "nanoflares" for detecting mRNA in living cells. Nano-flares take advantage of the highly efficient fluorescence quenching properties of gold, cellular uptake of oligonucleotide nanoparticle conjugates without the use of transfection agents, and the enzymatic stability of such conjugates, thus overcoming many of the challenges to creating sensitive and effective intracellular probes. Nano-flares exhibit high signaling, have low background fluorescence, and are sensitive to changes in the number of RNA transcripts present in cells.

Research paper thumbnail of Selective Enhancement of Nucleases by Polyvalent DNA-Functionalized Gold Nanoparticles

Journal of the American Chemical Society, 2011

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enh... more We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling proteinnanoparticle interactions.

Research paper thumbnail of Gene Regulation with Polyvalent siRNA−Nanoparticle Conjugates

Journal of the American Chemical Society, 2009

We report the synthesis and characterization of polyvalent RNA-gold nanoparticle conjugates (RNA-... more We report the synthesis and characterization of polyvalent RNA-gold nanoparticle conjugates (RNA-Au NPs), nanoparticles that are densely functionalized with synthetic RNA oligonucleotides and designed to function in the RNAi pathway. The particles were rationally designed and synthesized to be free of degrading enzymes, have a high surface loading of siRNA duplexes, and contain an auxiliary passivating agent for increased stability in biological media. The resultant conjugates have a half-life six times longer than free dsRNA, readily enter cells without the use of transfection agents, and demonstrate a high gene knockdown capability in a cell model.

Research paper thumbnail of Polyvalent Nucleic Acid Nanostructures

Journal of the American Chemical Society, 2011

Polyvalent oligonucleotide-nanoparticle conjugates possess several unique emergent properties inc... more Polyvalent oligonucleotide-nanoparticle conjugates possess several unique emergent properties including enhanced cellular uptake, high antisense bioactivity, and nuclease resistance, which hypothetically originate from the dense packing and orientation of oligonucleotides on the surface of the nanoparticle. In this communication, we describe a new class of polyvalent nucleic acid nanostructures (PNANs), which comprise only crosslinked and oriented nucleic acids. We demonstrate that these particles are capable of effecting high cellular uptake and gene regulation without the need of a cationic polymer co-carrier. The PNANs also exhibit cooperative binding behavior and nuclease resistance properties.

Research paper thumbnail of Multiplexed Nanoflares: mRNA Detection in Live Cells

Analytical Chemistry, 2012

We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of s... more We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are spherical nucleic acid (SNA) gold nanoparticle (Au NP) conjugates consisting of densely packed and highly oriented oligonucleotide sequences, many of which are hybridized to a reporter with a distinct fluorophore label and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra- and intracellular environments. Importantly, one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background. Compared to single-component nanoflares, these structures allow one to determine more precisely relative mRNA levels in individual cells, improving cell sorting and quantification.

Research paper thumbnail of Nano-flares for mRNA Regulation and Detection

ACS Nano, 2009

We build off the previously described concept of a nano-flare to develop an oligonucleotide gold ... more We build off the previously described concept of a nano-flare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose-and sequence-dependent manner and resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nano-flare and is a first step towards the development of an mRNA responsive 'theranostic'.

Research paper thumbnail of Nanoparticle shape anisotropy dictates the collective behavior of surface-bound ligands

We report on the modification of the properties of surface-confined ligands in nanoparticle syste... more We report on the modification of the properties of surface-confined ligands in nanoparticle systems through the introduction of shape anisotropy. Specifically, triangular gold nanoprisms, densely functionalized with oligonucleotide ligands, hybridize to complementary particles with an affinity that is several million times higher than that of spherical nanoparticle conjugates functionalized with the same amount of DNA. In addition, they exhibit association rates that are 2 orders of magnitude greater than those of their spherical counterparts. This phenomenon stems from the ability of the flat, extended facets of nonspherical nanoparticles to (1) support more numerous ligand interactions through greater surface contact with complementary particles, (2) increase the effective local concentration of terminal DNA nucleotides that mediate hybridization, and (3) relieve the conformational stresses imposed on nanoparticle-bound ligands participating in interactions between curved surfaces. Finally, these same trends are observed for the pH-mediated association of nanoparticles functionalized with carboxylate ligands, demonstrating the generality of these findings.

Research paper thumbnail of Tailoring DNA Structure To Increase Target Hybridization Kinetics on Surfaces

Journal of the American Chemical Society, Aug 11, 2010

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces... more We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.

Research paper thumbnail of Selective enhancement of nucleases by polyvalent DNA-functionalized gold nanoparticles

Journal of the American Chemical Society, Feb 1, 2011

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enh... more We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling proteinnanoparticle interactions.

Research paper thumbnail of Short Duplex Probes for Enhanced Target Hybridization

Research paper thumbnail of Polyvalent rna-nanoparticle compositions

Research paper thumbnail of Scavenger Receptors Mediate Cellular Uptake of Polyvalent Oligonucleotide-Functionalized Gold Nanoparticles

Bioconjugate Chemistry, 2010

Mammalian cells have been shown to internalize oligonucleotide-functionalized gold nanoparticles ... more Mammalian cells have been shown to internalize oligonucleotide-functionalized gold nanoparticles (DNA-Au NPs or siRNA-Au NPs) without the aid of auxiliary transfection agents and use them to initiate an antisense or RNAi response. Previous studies have shown that the dense monolayer of oligonucleotides on the nanoparticle leads to the adsorption of serum proteins and facilitates cellular uptake. Here, we show that serum proteins generally act to inhibit cellular uptake of DNA-Au NPs. We identify the pathway for DNA-Au NPs entry in HeLa cells.

Research paper thumbnail of Polyvalent DNA Nanoparticle Conjugates Stabilize Nucleic Acids

Nano Letters, 2009

Polyvalent oligonucleotide gold nanoparticle conjugates have unique fundamental properties includ... more Polyvalent oligonucleotide gold nanoparticle conjugates have unique fundamental properties including distance-dependent plasmon coupling, enhanced binding affinity, and the ability to enter cells and resist enzymatic degradation. Stability in the presence of enzymes is a key consideration for therapeutic uses; however the manner and mechanism by which such nanoparticles are able to resist enzymatic degradation is unknown. Here, we quantify the enhanced stability of polyvalent gold oligonucleotide nanoparticle conjugates with respect to enzyme-catalyzed hydrolysis of DNA and present evidence that the negatively charged surfaces of the nanoparticles and resultant high local salt concentrations are responsible for enhanced stability.

Research paper thumbnail of Nano-Flares:  Probes for Transfection and mRNA Detection in Living Cells

Journal of the American Chemical Society, 2007

We demonstrate that novel oligonucleotide-modified gold nanoparticle probes hybridized to fluorop... more We demonstrate that novel oligonucleotide-modified gold nanoparticle probes hybridized to fluorophore-labeled complements can be used as both transfection agents and cellular "nanoflares" for detecting mRNA in living cells. Nano-flares take advantage of the highly efficient fluorescence quenching properties of gold, cellular uptake of oligonucleotide nanoparticle conjugates without the use of transfection agents, and the enzymatic stability of such conjugates, thus overcoming many of the challenges to creating sensitive and effective intracellular probes. Nano-flares exhibit high signaling, have low background fluorescence, and are sensitive to changes in the number of RNA transcripts present in cells.

Research paper thumbnail of Selective Enhancement of Nucleases by Polyvalent DNA-Functionalized Gold Nanoparticles

Journal of the American Chemical Society, 2011

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enh... more We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling proteinnanoparticle interactions.

Research paper thumbnail of Gene Regulation with Polyvalent siRNA−Nanoparticle Conjugates

Journal of the American Chemical Society, 2009

We report the synthesis and characterization of polyvalent RNA-gold nanoparticle conjugates (RNA-... more We report the synthesis and characterization of polyvalent RNA-gold nanoparticle conjugates (RNA-Au NPs), nanoparticles that are densely functionalized with synthetic RNA oligonucleotides and designed to function in the RNAi pathway. The particles were rationally designed and synthesized to be free of degrading enzymes, have a high surface loading of siRNA duplexes, and contain an auxiliary passivating agent for increased stability in biological media. The resultant conjugates have a half-life six times longer than free dsRNA, readily enter cells without the use of transfection agents, and demonstrate a high gene knockdown capability in a cell model.

Research paper thumbnail of Polyvalent Nucleic Acid Nanostructures

Journal of the American Chemical Society, 2011

Polyvalent oligonucleotide-nanoparticle conjugates possess several unique emergent properties inc... more Polyvalent oligonucleotide-nanoparticle conjugates possess several unique emergent properties including enhanced cellular uptake, high antisense bioactivity, and nuclease resistance, which hypothetically originate from the dense packing and orientation of oligonucleotides on the surface of the nanoparticle. In this communication, we describe a new class of polyvalent nucleic acid nanostructures (PNANs), which comprise only crosslinked and oriented nucleic acids. We demonstrate that these particles are capable of effecting high cellular uptake and gene regulation without the need of a cationic polymer co-carrier. The PNANs also exhibit cooperative binding behavior and nuclease resistance properties.

Research paper thumbnail of Multiplexed Nanoflares: mRNA Detection in Live Cells

Analytical Chemistry, 2012

We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of s... more We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are spherical nucleic acid (SNA) gold nanoparticle (Au NP) conjugates consisting of densely packed and highly oriented oligonucleotide sequences, many of which are hybridized to a reporter with a distinct fluorophore label and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra- and intracellular environments. Importantly, one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background. Compared to single-component nanoflares, these structures allow one to determine more precisely relative mRNA levels in individual cells, improving cell sorting and quantification.

Research paper thumbnail of Nano-flares for mRNA Regulation and Detection

ACS Nano, 2009

We build off the previously described concept of a nano-flare to develop an oligonucleotide gold ... more We build off the previously described concept of a nano-flare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose-and sequence-dependent manner and resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nano-flare and is a first step towards the development of an mRNA responsive 'theranostic'.

Research paper thumbnail of Nanoparticle shape anisotropy dictates the collective behavior of surface-bound ligands

We report on the modification of the properties of surface-confined ligands in nanoparticle syste... more We report on the modification of the properties of surface-confined ligands in nanoparticle systems through the introduction of shape anisotropy. Specifically, triangular gold nanoprisms, densely functionalized with oligonucleotide ligands, hybridize to complementary particles with an affinity that is several million times higher than that of spherical nanoparticle conjugates functionalized with the same amount of DNA. In addition, they exhibit association rates that are 2 orders of magnitude greater than those of their spherical counterparts. This phenomenon stems from the ability of the flat, extended facets of nonspherical nanoparticles to (1) support more numerous ligand interactions through greater surface contact with complementary particles, (2) increase the effective local concentration of terminal DNA nucleotides that mediate hybridization, and (3) relieve the conformational stresses imposed on nanoparticle-bound ligands participating in interactions between curved surfaces. Finally, these same trends are observed for the pH-mediated association of nanoparticles functionalized with carboxylate ligands, demonstrating the generality of these findings.

Research paper thumbnail of Tailoring DNA Structure To Increase Target Hybridization Kinetics on Surfaces

Journal of the American Chemical Society, Aug 11, 2010

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces... more We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.