Article
Chemistry, Multidisciplinary
Federico Pini, Laura Frances-Soriano, Vittoria Andrigo, Marta Maria Natile, Niko Hildebrandt
Summary: The main challenge for UCNPs is to optimize their implementation in FRET biosensing and bioimaging for highly sensitive, wash-free, multiplexed, accurate, and precise quantitative analysis of biomolecules and biomolecular interactions. We have developed an analytical model that can determine the ideal UCNP-FRET system within a short period of time, resulting in significant improvements in sensitivity.
Article
Chemistry, Applied
Yoliztli Banales-Leal, Andrea Garcia-Rodriguez, Fabian Cuetara-Guadarrama, Mireille Vonlanthen, Kendra Sorroza-Martinez, David Morales-Morales, Ernesto Rivera
Summary: A novel series of dendritic compounds with peripheral pyrene groups and a porphyrin core were synthesized and characterized in this study. Metallation with Zn(II) and Mg(II) resulted in red shifts in the Soret absorption band and blue shifts in the emission band for the dendritic porphyrins, with all compounds exhibiting high energy transfer efficiency.
Article
Chemistry, Analytical
Pingping Ji, Guimei Han, Yan Huang, Hongxin Jiang, Qiwen Zhou, Xiaowei Liu, Deming Kong
Summary: A fluorescent sensing strategy using Pb2+ DNAzyme-controlled tetrahedral DNA nanostructure (TDN)-mediated hyper-branched hybridization chain reaction (hHCR) has been developed for rapid, highly sensitive, and specific detection of lead (II) ion. The method demonstrates ultrahigh sensitivity, strong anti-interference capacity, and short detection time, showing great potential for practical applications.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Jinlu Tang, Bo Li, Cuihua Qi, Zhaoting Wang, Kai Yin, Linyan Guo, Weihang Zhang, Baoyin Yuan
Summary: Sialylation is crucial in physiological processes, with aberrant sialylation being linked to disease development, particularly in cancer. A DNA dendrimer-assisted FRET strategy was developed to image specific cell-surface sialylation effectively, demonstrating significant improvement in FRET intensity and successful imaging in cancer cells.
Article
Chemistry, Analytical
Hongkun Li, Yuqi Zhang, Guifen Jie
Summary: A DNA reticular nanostructure was assembled using hairpin DNA probes via a target-induced circular amplification strategy for the fluorescence biosensing of miRNA-21. This method allows sensitive detection of miRNA-21 and holds great application potential in biosensors and functional nanomaterials.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Chemistry, Multidisciplinary
Hsin-Yun Tsai, W. Russ Algar
Summary: Forster resonance energy transfer (FRET) is widely used for biological probes and sensors. Concentric FRET (cFRET) probes enable multiplexed sensing with a single vector. This study demonstrates that dendrimers labeled with a luminescent terbium complex (Tb) can be a viable alternative platform for cFRET probes. This dendrimer-based architecture shows the importance of cFRET for the development of a new generation of probes for biological sensing.
Article
Chemistry, Physical
Hiromu Kashida, Hayato Kawai, Hidenori Azuma, Yasuyuki Araki, Takehiko Wada, Hiroyuki Asanuma
Summary: By utilizing a DNA scaffold to analyze homo-FRET between pyrene moieties, the efficiency of energy transfer was successfully detected with excellent agreement to Forster theory. These findings will guide the design of novel molecular probes and light-harvesting antennae.
Article
Chemistry, Analytical
Zuhao Zhang, Lu Zhang, Shujing Wang, Ruifang Liu, Li Li, Peini Zhao, Chaomin Gao, Fengming Chen, Shenguang Ge, Jinghua Yu
Summary: A CRISPR/Cas12a electrochemiluminescence biosensor was developed for ultrasensitive detection of miRNA-21. The biosensor utilized Tribulus terrestris-like AuCu nanoterrestris and DNA tetrahedral nanostructures, and employed a multiple sites DNA walker for signal amplification, achieving efficient detection.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Multidisciplinary
V. Siva Rama Krishna, Soumen Adak, Palash Jana, Varun Bheemireddy, Subhajit Bandyopadhyay
Summary: The study reports a supramolecular dendrimer-dye assembly that mimics the natural light-harvesting mechanism, where a molecule self-aggregates in water into micelles encapsulating a dye and efficiently transfers energy to the dye reaction center. The energy transfer process has been studied using steady-state and time-resolved fluorescence spectroscopy, with molecular dynamics simulations in agreement with experimental observations.
CHEMISTRY-AN ASIAN JOURNAL
(2021)
Article
Chemistry, Physical
Matthew Chiriboga, Sebastian A. Diaz, Divita Mathur, David A. Hastman, Joseph S. Melinger, Remi Veneziano, Igor L. Medintz
Summary: Progress has been made using DNA to template J-aggregates, which exhibit interesting photonic properties and enhance exciton transfer. Linear contiguous J-aggregates can relay excitons up to 16.3 nm, however, nonlinear arrays show poor exciton transfer efficiency.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biophysics
Ling Liang, Yong Jian Jiang, Long Chuan Zhang, Hui Liu, Yuan Fang Li, Chun Mei Li, Cheng Zhi Huang
Summary: In this study, a two-dimensional DNA walking nanomachine with high working efficiency and low cost was easily assembled using GO as the working platform. The nanomachine showed simple operation, high cost-performance ratio, and low background signal, making it highly promising for biosensing applications.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Analytical
Jiehua Ma, JianSheng Zhu, Jingyun Li, Yucai Yang
Summary: The study demonstrates that an inverted tetrahedral DNA nanostructure (iTDN) can serve as a cost-effective interfacial probe for electrochemical sensing, with only one thiol group needed for detection. Due to the multiple recognition elements, appropriate orientation, and high sensitivity of iTDNs, they have the potential application in detecting different analytes with high specificity in complex media.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Izabela Kaminska, Johann Bohlen, Renukka Yaadav, Patrick Schueler, Mario Raab, Tim Schroeder, Jonas Zaehringer, Karolina Zielonka, Stefan Krause, Philip Tinnefeld
Summary: Graphene is a game-changing material with unique mechanical and electrical properties. This study highlights its application as a transparent yet fluorescence-quenching energy transfer acceptor, showcasing its versatility in various fields such as molecular height determination, DNA structure visualization, and orientation determination of energy transfer pairs.
ADVANCED MATERIALS
(2021)
Review
Pharmacology & Pharmacy
Veronica Folliero, Carla Zannella, Annalisa Chianese, Debora Stelitano, Annalisa Ambrosino, Anna De Filippis, Marilena Galdiero, Gianluigi Franci, Massimiliano Galdiero
Summary: Dendrimers are nanoscale structures with defined characteristics that offer many advantages in the treatment of parasitic infections, including reducing drug dosage and minimizing side effects. In recent years, significant progress has been made in therapeutic, prophylactic, and diagnostic applications of dendrimers for managing parasitic diseases.
Review
Chemistry, Analytical
Wanyu Xu, Hui Chen, Yang Li, Shuangna Liu, Kemin Wang, Jianbo Liu
Summary: This review focuses on the design and applications of DNA-based artificial transmembrane channels. DNA serves as the main scaffold material for the design of these channels, utilizing two structural modules for mass transportation and membrane immobilization. Various types of DNA transmembrane channels are systematically summarized, and efforts to utilize them in biosensor and biomedical applications are discussed. The challenges and future developments in the field of artificial transmembrane channel research are also highlighted.
Article
Nanoscience & Nanotechnology
David A. Hastman, Parth Chaturvedi, Eunkeu Oh, Joseph S. Melinger, Igor L. Medintz, Lela Vukovic, Sebastian A. Diaz
Summary: This study investigates the impact of local temperature changes on the dehybridization of double-stranded DNA. By varying the distance between DNA and nanoparticles as well as the energy fluence of laser pulses, the researchers achieve control over the dehybridization rate and release of DNA.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Matthew Chiriboga, Sebastian A. Diaz, Divita Mathur, David A. Hastman, Joseph S. Melinger, Remi Veneziano, Igor L. Medintz
Summary: Progress has been made using DNA to template J-aggregates, which exhibit interesting photonic properties and enhance exciton transfer. Linear contiguous J-aggregates can relay excitons up to 16.3 nm, however, nonlinear arrays show poor exciton transfer efficiency.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Public, Environmental & Occupational Health
Harapan Harapan, Samsul Anwar, Amanda Yufika, Khan Sharun, Mahir Gachabayov, Marhami Fahriani, Milda Husnah, Rawan Raad, Rashed Y. A. Abdalla, Rashed Y. Adam, Namareg M. E. Khiri, Mohajer I. H. Ismaeil, Asma Y. Ismail, Wajdi Kacem, Nesrine B. H. Dahman, Zeineb Teyeb, Khaoula Aloui, Montacer Hafsi, Manel Ferjani, Dalia A. Deeb, Dina Emad, Kirellos Said Abbas, Fatma A. Monib, Farah S. Sami, R. Subramaniam, Suhrud Panchawagh, Sunil Anandu, Md Ariful Haque, Lirane E. D. Ferreto, Maria F. C. Briones, Rocio B. Morales, Sebastian A. L. Diaz, Jose T. O. Aburto, Jorge E. T. Rojas, Emmanuel O. Balogun, Seyi S. Enitan, Akele R. Yomi, Abiodun Durosinmi, Eyiuche D. Ezigbo, Esther N. Adejumo, Elham Babadi, Edris Kakemam, Najma Malik, Irfan Ullah, Dott F. Rosiello, Talha B. Emran, Guilherme W. Wendt, Morteza Arab-Zozani, Abram L. Wagner, Mudatsir Mudatsir
Summary: The study aimed to determine the level of vaccine hesitancy in communities, finding that belief in vaccination benefits and concerns about new vaccines were still prevalent in 10 countries in Asia, Africa, and South America.
PATHOGENS AND GLOBAL HEALTH
(2022)
Article
Chemistry, Physical
Azhad U. Chowdhury, Sebastian A. Diaz, Jonathan S. Huff, Matthew S. Barclay, Matthew Chiriboga, Gregory A. Ellis, Divita Mathur, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Paul D. Cunningham, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Igor L. Medintz, Joseph S. Melinger, Ryan D. Pensack
Summary: By altering the spatial configuration of dyes on a DNA template, we can tune the energy transfer and quenching between molecular excitons. We find that heterodimers with different spatial configurations exhibit different optical properties, which is significant for various applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Matthew Chiriboga, Christopher M. Green, David A. Hastman, Divita Mathur, Qi Wei, Sebastian A. Diaz, Igor L. Medintz, Remi Veneziano
Summary: In this study, we propose a method using the YOLO modern object detection platform to rapidly identify correctly formed DNA nanostructures in atomic force microscope images. The approach is flexible and can be easily adapted to various structural geometries. Experimental results demonstrate high accuracy in identifying structures from raw images.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Jonathan S. Huff, Sebastian A. Diaz, Matthew S. Barclay, Azhad U. Chowdhury, Matthew Chiriboga, Gregory A. Ellis, Divita Mathur, Lance K. Patten, Simon K. Roy, Aaron Sup, Austin Biaggne, Brian S. Rolczynski, Paul D. Cunningham, Lan Li, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Igor L. Medintz, Daniel B. Turner, Joseph S. Melinger, Ryan D. Pensack
Summary: In this study, DNA Holliday junctions were used to assemble aggregates of different ratios of cyanine dyes Cy5 and Cy5.5, allowing control over the energy position of the absorption features. The assembled aggregates exhibited shorter excited-state lifetimes and quenched emission compared to the monomeric dyes. A purely electronic exciton theory model was used to describe the properties of the aggregates, and the potential advantages of an idealized J-aggregate based on Förster resonance energy transfer (FRET) were discussed.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Multidisciplinary
Christopher M. Green, Joseph Spangler, Kimihiro Susumu, David A. Stenger, Igor L. Medintz, Sebastian A. Diaz
Summary: This article introduces the strategies of utilizing CRISPR/Cas nucleases Cas13 and Cas12 for the development of highly sensitive and rapid diagnostic assays. By using quantum dots and nucleic acid hairpin, the highly luminescent and colorimetric molecular beacons were assembled, achieving pM-level detection of target DNA and RNA without nucleotide amplification. The authors also demonstrated the capabilities of multiplexing and camera-phone detection.
Article
Chemistry, Multidisciplinary
Sebastian A. Diaz, Gissela Pascual, Lance K. Patten, Simon K. Roy, Adam Meares, Matthew Chiriboga, Kimihiro Susumu, William B. Knowlton, Paul D. Cunningham, Divita Mathur, Bernard Yurke, Igor L. Medintz, Jeunghoon Lee, Joseph S. Melinger
Summary: Understanding and controlling exciton coupling in dye aggregates is important for potential applications such as coherent exciton devices, nanophotonics, and biosensing. DNA nanostructure templates provide a powerful modular approach. In this study, Cy5-R dyes were used to examine the formation and properties of 30 unique DNA templated homodimers, revealing the role of sterics and hydrophobicity in determining the orientation and coupling strength of the dimers.
Article
Chemistry, Physical
Brian S. S. Rolczynski, Sebastian A. Diaz, Young C. C. Kim, Divita Mathur, William P. P. Klein, Igor L. L. Medintz, Joseph S. S. Melinger
Summary: This study uses structural DNA nanotechnology to investigate energy-transport mechanisms and interactions in a chromophore network. By introducing variations in a 14-Site chromophore network, machine-learning algorithms and spectroscopy measurements were used to determine the roles of each Site. Molecular dynamics simulations and energy-transport modeling were also performed to understand the physical significance of these patterns. The study provides insights into the understanding of each Site's role in an optoelectronic molecular network using machine-learning methods.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
Divita Mathur, Meghna Thakur, Sebastian A. Diaz, Kimihiro Susumu, Michael H. Stewart, Eunkeu Oh, Scott A. Walper, Igor L. Medintz
Summary: Cell-free synthetic biology is a valuable tool for developing portable biosensors. By using a modular quantum dot-based reporter platform, it is possible to detect multiple analytes simultaneously.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Analytical
Matthew Chiriboga, Christopher M. Green, Divita Mathur, David A. Hastman, Joseph S. Melinger, Remi Veneziano, Igor L. Medintz, Sebastian A. Diaz
Summary: Coherently coupled pseudoisocyanine (PIC) dye aggregates, formed through heterogeneous nucleation on DNA oligonucleotides, exhibit unique photophysical properties that differ from previously reported aggregates. This new type of aggregate, called the super aggregate (SA), displays peak narrowing and quantum yield variation in emission spectra, indicative of stronger coupling. Characterization with circular dichroism and atomic force microscopy further reveals unique features depending on the DNA substrate. By integrating an energy transfer acceptor, the SA demonstrates mixed energy transfer characteristics depending on the DNA's sequence and geometry. These findings suggest that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate, informing rational design principles for future device prototyping.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2023)
Article
Multidisciplinary Sciences
Joyce C. C. Breger, James N. N. Vranish, Eunkeu Oh, Michael H. H. Stewart, Kimihiro Susumu, Guillermo Lasarte-Aragone's, Gregory A. A. Ellis, Scott A. A. Walper, Sebastian A. Diaz, Shelby L. L. Hooe, William P. P. Klein, Meghna Thakur, Mario G. G. Ancona, Igor L. L. Medintz
Summary: Enzymes in multistep cascades can self-assemble with nanoparticles into nanoclusters, allowing for directed substrate transport and significant improvement in catalytic flux. Efficiency of the channeling can be enhanced by optimizing enzymatic stoichiometry, using two-dimensional nanoplatelets, and ordering the enzyme assembly. Detailed analyses confirm the formation of the assembly and clarify the structure-function properties, verifying the generalized applicability of these self-assembled biocatalytic nanoclusters.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
David A. Hastman, Eunkeu Oh, Joseph S. Melinger, Christopher M. Green, Aaron J. P. Thielemann, Igor L. Medintz, Sebastian A. Diaz
Summary: This study investigates the effect of plasmonic gold nanoparticle (AuNP) size on the rate of thermal release of single-stranded oligonucleotides under femtosecond (fs)-pulsed laser irradiation. Contrary to theoretical predictions, smaller AuNP diameters lead to faster DNA denaturation rates. Controlling for other factors yields the same result, suggesting that direct energy transfer may play a significant role as AuNPs decrease in size.
Proceedings Paper
Biochemical Research Methods
Christopher M. Green, Joseph Spangler, Kimihiro Susumu, David A. Stenger, Igor L. Medintz, Sebastian A. Diaz
Summary: Colloidal quantum dots are used for various applications due to their high luminosity and large surface areas for bioconjugation. We have developed a method to conjugate nucleic acids to quantum dots using chimeric peptide-PNA and characterized QD-FRET reporters for CRISPR/Cas nuclease assays. We identified factors that could limit the sensitivity of these reporters in practice.
COLLOIDAL NANOPARTICLES FOR BIOMEDICAL APPLICATIONS XVIII
(2023)
Review
Chemistry, Multidisciplinary
Divita Mathur, Sebastian A. Diaz, Niko Hildebrandt, Ryan D. Pensack, Bernard Yurke, Austin Biaggne, Lan Li, Joseph S. Melinger, Mario G. Ancona, William B. Knowlton, Igor L. Medintz
Summary: DNA nanotechnology enables the self-assembly of 3D nanoscale structures, with potential applications in various fields. These structures can be modified and used as optical substrates. Dynamic DNA structures have the ability to reconfigure and change their properties, allowing for multiple applications.
CHEMICAL SOCIETY REVIEWS
(2023)