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  • 1.
    Machado, Isabel
    et al.
    SOMAprobes, Spain.
    Garrido, Victoria
    CSIC UPNa Gobierno Navarra, Spain.
    Hernandez, Luiza
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. SOMAprobes, Spain.
    Botero, Juliana
    SOMAprobes, Spain.
    Bastida, Nora
    SOMAprobes, Spain.
    San-Roman, Beatriz
    CSIC UPNa Gobierno Navarra, Spain.
    Grillo, Maria-Jesus
    CSIC UPNa Gobierno Navarra, Spain.
    Hernandez, Frank
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes2019In: Analytica Chimica Acta, ISSN 0003-2670, E-ISSN 1873-4324, Vol. 1054, p. 157-166Article in journal (Refereed)
    Abstract [en]

    Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carriers of the pathogenic Salmonella for humans. To prevent this relevant zoonosis, key changes in food safety regulations were undertaken to improve controls in the food production chain. Despite these measures, large outbreaks of salmonellosis were reported worldwide in the last decade. Thus, new strategies for Salmonella detection are a priority for both, food safety and public health authorities. Such detection systems should provide significant reduction in diagnostic time (hours) compared to the currently available methods (days). Herein, we report on the discovery and characterization of nucleic acid probes for the sensitive and specific detection of live Salmonella within less than 8 h of incubation. We are the first to postulate the nuclease activity derived from Salmonella as biomarker of infection and its utility to develop innovative detection strategies. Our results have shown the screening and identification of two oligonucleotide sequences (substrates) as the most promising probes for detecting Salmonella - Sal-3 and Sal-5. The detection limits for both probes were determined with the reference Salmonella Typhimurium (STM 1) and Salmonella Enteritidis (SE 1) cultures. Sal-3 has reported LOD values around 10(5) CFU mL(-1) for STM 1 and 10(4) CFU mL(-1) for SE 1, while Sal-5 proves to be a slightly better probe, with LODs of 10(4) CFU mL(-1) for STM 1 and 10(4) CFU mL(-1) for SE 1. Both selected probes have shown the capability to recognize 49 out of 51 different Salmonella serotypes tested in vitro and the most frequent serotypes in porcine mesenteric lymph nodes as a standard sample used in fattening-pig salmonellosis baseline studies. Notably, our results showed 100% correlation between nuclease detection and the PCR-InvA or ISO-6579 standard method, underlining the great potential of this innovative nucleic acids technology to be implemented as a rapid method for food safety testing. (C) 2018 Elsevier B.V. All rights reserved.

    The full text will be freely available from 2019-12-21 15:32
  • 2.
    Rivilla, Ivan
    et al.
    Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Donostia International Physics Center (DIPC), Donostia/San Sebastián, Spain.
    de Cozar, Abel
    Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Donostia International Physics Center (DIPC), Donostia/San Sebastián, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
    Schafer, Thomas
    Ikerbasque, Basque Foundation for Science, Bilbao, Spain; NanoBioSeparations Group, POLYMAT University of the Basque Country (UPV/EHU), Donostia/San Sebastián, Spain.
    Hernandez, Frank J.
    NanoBioSeparations Group, POLYMAT University of the Basque Country (UPV/EHU), Avda. Tolosa 72, E-20018 Donostia/San Sebastián, Spain.
    Bittner, Alexander M.
    NanoBioSeparations Group, POLYMAT University of the Basque Country (UPV/EHU), Donostia/San Sebastián, Spain; CIC NanoGUNE, Donostia/San Sebastián, Spain.
    Eleta-Lopez, Aitziber
    CIC NanoGUNE, Donostia/San Sebastián, Spain.
    Aboudzadeh, Ali
    NanoBioSeparations Group, POLYMAT University of the Basque Country (UPV/EHU), Donostia/San Sebastián, Spain.
    Santos, Jose I.
    SGIker NMR Facility, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Donostia/San Sebastián, Spain.
    Miranda, Jose I.
    SGIker NMR Facility, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Donostia/San Sebastián, Spain.
    Cossio, Fernando P.
    Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Donostia International Physics Center (DIPC), Donostia/San Sebastián, Spain .
    Catalysis of a 1,3-dipolar reaction by distorted DNA incorporating a heterobimetallic platinum(ii) and copper(ii) complex2017In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 8, no 10, p. 7038-7046Article in journal (Refereed)
    Abstract [en]

    A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N-metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [[small pi]4s + [small pi]2s] mechanisms leading to the exclusive formation of racemic endo-cycloadducts.

  • 3.
    Hernandez, Luiza I
    et al.
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian, Spain.
    Ozalp, Veli Cengiz
    School of Medicine, Istanbul Kemerburgaz University, Istanbul, Turkey.
    Hernandez, Frank J
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian, Spain.
    Nuclease activity as a specific biomarker for breast cancer.2016In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 52, no 83, p. 12346-12349Article in journal (Refereed)
    Abstract [en]

    We report on the activity of nucleases derived from cancer cells as a means for specific targeting using nucleic acid probes (substrates). We hypothesize that cancer cells can be differentiated from healthy cells based on their nuclease activity profile, and thus, any method based on this property represents a novel alternative for diagnostic and therapeutic intervention.

  • 4.
    Özalp, V Cengiz
    et al.
    School of Medicine, Istanbul Kemerburgaz University, Istanbul, 34217, Turkey.
    Çam, Dilek
    Department of Biotechnology, Middle East Technical University, Turkey.
    Hernandez, Frank J
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian 20009, Spain.
    Hernandez, Luiza I
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian 20009, Spain.
    Schäfer, Thomas
    Polymat, University of the Basque Country UPV, San Sebastian-Donostia, Spain.
    Öktem, Hüseyin A
    Department of Biotechnology, Middle East Technical University, Turkey; Nanobiz R&D Ltd., Galium Bld. No. 18, METU Science Park, 06800 Ankara, Turkey.
    Small molecule detection by lateral flow strips via aptamer-gated silica nanoprobes.2016In: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 141, no 8, p. 2595-9Article in journal (Refereed)
    Abstract [en]

    A fast, sensitive and ratiometric biosensor strategy for small molecule detection was developed through nanopore actuation. The new platform engineers together, a highly selective molecular recognition element, aptamers, and a novel signal amplification mechanism, gated nanopores. As a proof of concept, aptamer gated silica nanoparticles have been successfully used as a sensing platform for the detection of ATP concentrations at a wide linear range from 100 μM up to 2 mM.

  • 5.
    Borsa, Baris A
    et al.
    Istanbul Kemerburgaz University, School of Medicine, Istanbul 34217, Turkey.
    Tuna, Bilge G
    Yeditepe University, School of Medicine, Department of Biophysics, Istanbul Turkey.
    Hernandez, Frank J
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian 20009, Spain.
    Hernandez, Luiza I
    SOMAprobes S.L., Science and Technology Park of Gipuzkoa, San Sebastian 20009, Spain.
    Bayramoglu, Gulay
    Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Ankara, Turkey; Department of Chemistry, Faculty of Sciences, Gazi University, 06500 Ankara, Turkey.
    Arica, M Yakup
    Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Ankara, Turkey.
    Ozalp, V Cengiz
    Istanbul Kemerburgaz University, School of Medicine, Istanbul 34217, Turkey.
    Staphylococcus aureus detection in blood samples by silica nanoparticle-oligonucleotides conjugates.2016In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 86, p. 27-32Article in journal (Refereed)
    Abstract [en]

    A fast, specific and sensitive homogeneous assay for Staphylococcus aureus detection was developed by measuring the activity of secreted nuclease from the bacteria via a modified DNA oligonucleotide. As biosensor format, an effective system, Nanokeepers as previously reported, were used for triggered release of confined fluorophores, and hence specific detection of S. aureus on nuclease activity was obtained. The interference from blood components for fluorescent quantification was eliminated by a pre-purification by aptamer-functionalized silica magnetic nanoparticles. The reported assay system was exclusively formed by nucleic acid oligos and magnetic or mesoporous silica nanoparticles, that can be used on blood samples in a stepwise manner. The assay was successfully used as a sensing platform for the specific detection of S. aureus cells as low as 682 CFU in whole blood.

  • 6.
    Hernandez, Luiza I
    et al.
    Biodonostia Research Institute, San Sebastian, Spain.
    Machado, Isabel
    POLYMAT, University of the Basque Country UPV/EHU, San Sebastian, Spain.
    Schäfer, Thomas
    POLYMAT, University of the Basque Country UPV/EHU, San Sebastian, Spain.
    Hernandez, Frank J
    Biodonostia Research Institute, San Sebastian, Spain; POLYMAT, University of the Basque Country UPV/EHU, San Sebastian, Spain.
    Aptamers overview: selection, features and applications.2015In: Current Topics in Medicinal Chemistry, ISSN 1568-0266, E-ISSN 1873-4294, Vol. 15, no 12, p. 1066-1081Article in journal (Refereed)
    Abstract [en]

    Apatamer technology has been around for a quarter of a century and the field had matured enough to start seeing real applications, especially in the medical field. Since their discovery, aptamers rapidly emerged as key players in many fields, such as diagnostics, drug discovery, food science, drug delivery and therapeutics. Because of their synthetic nature, aptamers are evolving at an exponential rate gaining from the newest advances in chemistry, nanotechnology, biology and medicine. This review is meant to give an overview of the aptamer field, by including general aspects of aptamer identification and applications as well as highlighting certain features that contribute to their quick deployment in the biomedical field.

  • 7.
    Hernandez, Frank J
    Biodonostia Research Institute, San Sebastian, Spain.
    Hernandez, Luiza I.
    Biodonostia Research Institute, San Sebastian, Spain.
    Ozalp, Veli C.
    Istanbul Kemerburgaz University, School of Medicine, Istanbul, Turkey.
    Nanocapsules in biomedicine: promises and challenges2015In: Advanced Theranostics Materials / [ed] Ashutosh Tiwari et al, John Wiley & Sons, 2015Chapter in book (Other academic)
  • 8.
    Hernandez, Frank J
    et al.
    POLYMAT, University of of Basque Country UPV/EHU, Avda. Tolosa 72, 20018 Donostia-San-Sebastián, Spain.
    Hernandez, Luiza I.
    Nanobiz Ltd., METU Technopark, Ankara 06800, Turkey.
    Kavruk, Murat
    Test and Calibration Center, Turkish Standards Institute (TSE), Gebze Kocaeli 41400, Turkey.
    Arica, Yakup M.
    Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Teknikokullar, Ankara, Turkey.
    Bayramoǧlu, Gülay
    Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Teknikokullar, Ankara, Turkey.
    Borsa, Baris A.
    School of Medicine, Istanbul Kemerburgaz University, 34217 Istanbul, Turkey.
    Öktem, Hüseyin A.
    Nanobiz Ltd., METU Technopark, Ankara 06800, Turkey.
    Schäfer, Thomas
    POLYMAT, University of of Basque Country UPV/EHU, Avda. Tolosa 72, 20018 Donostia-San-Sebastián, Spain.
    Özalp, Veli C.
    School of Medicine, Istanbul Kemerburgaz University, 34217 Istanbul, Turkey.
    NanoKeepers: stimuli responsive nanocapsules for programmed specific targeting and drug delivery2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 67, p. 9489-9492Article in journal (Refereed)
    Abstract [en]

    Bacterial resistance is a high priority clinical issue worldwide. Thus, an effective system that rapidly provides specific treatment for bacterial infections using controlled dose release remains an unmet clinical need. Herein, we report on the NanoKeepers approach for the specific targeting of S. aureus with controlled release of antibiotics based on nuclease activity. This journal is © the Partner Organisations 2014.

  • 9.
    Hernandez, Frank J
    et al.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Huang, Lingyan
    Integrated DNA Technologies (IDT), Coralville, IA, United States.
    Olson, Michael E.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Powers, Kristy M.
    Integrated DNA Technologies (IDT), Coralville, IA, United States.
    Hernandez, Luiza I.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Meyerholz, David K.
    Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Thedens, Daniel R.
    Department of Radiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Behlke, Mark A.
    Integrated DNA Technologies (IDT), Coralville, IA, United States.
    Horswill, Alexander R.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Mcnamara II, James O.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Noninvasive imaging of Staphylococcus aureus infections with a nuclease-activated probe2014In: Nature Medicine, ISSN 1078-8956, E-ISSN 1546-170X, Vol. 20, no 3, p. 301-306Article in journal (Refereed)
    Abstract [en]

    Technologies that enable the rapid detection and localization of bacterial infections in living animals could address an unmet need for infectious disease diagnostics. We describe a molecular imaging approach for the specific, noninvasive detection of S. aureus based on the activity of the S. aureus secreted nuclease, micrococcal nuclease (MN). Several short synthetic oligonucleotides, rendered resistant to mammalian serum nucleases by various chemical modifications and flanked with a fluorophore and quencher, were activated upon degradation by purified MN and in S. aureus culture supernatants. A probe consisting of a pair of deoxythymidines flanked by several 2′-O-methyl-modified nucleotides was activated in culture supernatants of S. aureus but not in culture supernatants of several other pathogenic bacteria. Systemic administration of this probe to mice bearing S. aureus muscle infections resulted in probe activation at the infection sites in an MN-dependent manner. This new bacterial imaging approach has potential clinical applicability for infections with S. aureus and several other medically important pathogens. © 2014 Nature America, Inc.

  • 10.
    Kiedrowski, Megan R.
    et al.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Crosby, Heidi A.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Hernandez, Frank J
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Malone, Cheryl L.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    McNamara II, James O.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Horswill, Alexander R.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Staphylococcus aureus Nuc2 is a functional, surface-attached extracellular nuclease2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 4, article id e95574Article in journal (Refereed)
    Abstract [en]

    Staphylococcus aureus is a prominent bacterial pathogen that causes a diverse range of acute and chronic infections. Recently, it has been demonstrated that the secreted nuclease (Nuc) enzyme is a virulence factor in multiple models of infection, and in vivo expression of nuc has facilitated the development of an infection imaging approach based on Nuc-activatable probes. Interestingly, S. aureus strains encode a second nuclease (Nuc2) that has received limited attention. With the growing interest in bacterial nucleases, we sought to characterize Nuc2 in more detail through localization, expression, and biochemical studies. Fluorescence microscopy and alkaline phosphatase localization approaches using Nuc2-GFP and Nuc2-PhoA fusions, respectively, demonstrated that Nuc2 is membrane bound with the C-terminus facing the extracellular environment, indicating it is a signal-anchored Type II membrane protein. Nuc2 enzyme activity was detectable on the S. aureus cell surface using a fluorescence resonance energy transfer (FRET) assay, and in time courses, both nuc2 transcription and enzyme activity peaked in early logarithmic growth and declined in stationary phase. Using a mouse model of S. aureus pyomyositis, Nuc2 activity was detected with activatable probes in vivo in nuc mutant strains, demonstrating that Nuc2 is produced during infections. To assess Nuc2 biochemical properties, the protein was purified and found to cleave both single- and double-stranded DNA, and it exhibited thermostability and calcium dependence, paralleling the properties of Nuc. Purified Nuc2 prevented biofilm formation in vitro and modestly decreased biomass in dispersal experiments. Altogether, our findings confirm that S. aureus encodes a second, surface-attached and functional DNase that is expressed during infections and displays similar biochemical properties to the secreted Nuc enzyme. © 2014 Kiedrowski et al.

  • 11.
    Dassie, Justin P.
    et al.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Hernandez, Luiza I.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Thomas, Gregory S.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Long, Matthew E.
    Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA, United States; Inflammation Program, University of of Iowa, Iowa City, IA, United States.
    Rockey, William M.
    Department of Radiation Oncology, University of of Iowa, Iowa City, IA, United States.
    Howell, Craig A.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Chen, Yani
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Hernandez, Frank J
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Liu, Xiu Y.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Wilson, Mary E.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States; Department of Microbiology, University of of Iowa, Iowa City, IA, United States; Veterans Affairs Medical Center, University of of Iowa, Iowa City, IA, United States.
    Allen, Lee-Ann
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States; Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA, United States; Inflammation Program, University of of Iowa, Iowa City, IA, United States; Department of Microbiology, University of of Iowa, Iowa City, IA, United States; Veterans Affairs Medical Center, University of of Iowa, Iowa City, IA, United States.
    Vaena, Daniel A.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States.
    Meyerholz, David K.
    Department of Pathology, University of of Iowa, Iowa City, IA, United States.
    Giangrande, Paloma H.
    Department of Internal Medicine, University of of Iowa, 375 Newton Rd, 5202 MERF, Iowa City, IA, United States; Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA, United States; Department of Radiation Oncology, University of of Iowa, Iowa City, IA, United States.
    Targeted inhibition of prostate cancer metastases with an RNA aptamer to prostate-specific membrane antigen2014In: Molecular Therapy, ISSN 1525-0016, E-ISSN 1525-0024, Vol. 22, no 11, p. 1910-1922Article in journal (Refereed)
    Abstract [en]

    Cell-targeted therapies (smart drugs), which selectively control cancer cell progression with limited toxicity to normal cells, have been developed to effectively treat some cancers. However, many cancers such as metastatic prostate cancer (PC) have yet to be treated with current smart drug technology. Here, we describe the thorough preclinical characterization of an RNA aptamer (A9g) that functions as a smart drug for PC by inhibiting the enzymatic activity of prostate-specific membrane antigen (PSMA). Treatment of PC cells with A9g results in reduced cell migration/invasion in culture and metastatic disease in vivo. Importantly, A9g is safe in vivo and is not immunogenic in human cells. Pharmacokinetic and biodistribution studies in mice confirm target specificity and absence of non-specific on/off-target effects. In conclusion, these studies provide new and important insights into the role of PSMA in driving carcinogenesis and demonstrate critical endpoints for the translation of a novel RNA smart drug for advanced stage PC. © The American Society of Gene amp; Cell Therapy.

  • 12.
    Hernandez, Luiza I.
    et al.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    Flenker, Katie S.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    Hernandez, Frank J
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    Klingelhutz, Aloysius J.
    Department of Microbiology, University of of Iowa, Iowa City, IA 52242, United States; Department of Radiation Oncology, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    McNamara, James O.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    Giangrande, Paloma H.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; Department of Radiation Oncology, University of of Iowa, Iowa City, IA 52242, United States; University of of Iowa, Iowa City, IA 52242, United States.
    Methods for evaluating cell-specific, cell-internalizing RNA aptamers2013In: Pharmaceuticals, ISSN 1424-8247, E-ISSN 1424-8247, Vol. 6, no 3, p. 295-319Article in journal (Refereed)
    Abstract [en]

    Recent clinical trials of small interfering RNAs (siRNAs) highlight the need for robust delivery technologies that will facilitate the successful application of these therapeutics to humans. Arguably, cell targeting by conjugation to cell-specific ligands provides a viable solution to this problem. Synthetic RNA ligands (aptamers) represent an emerging class of pharmaceuticals with great potential for targeted therapeutic applications. For targeted delivery of siRNAs with aptamers, the aptamer-siRNA conjugate must be taken up by cells and reach the cytoplasm. To this end, we have developed cell- based selection approaches to isolate aptamers that internalize upon binding to their cognate receptor on the cell surface. Here we describe methods to monitor for cellular uptake of aptamers. These include: (1) antibody amplification microscopy, (2) microplate- based fluorescence assay, (3) a quantitative and ultrasensitive internalization method (QUSIM) and (4) a way to monitor for cytoplasmic delivery using the ribosome inactivating protein-based (RNA-RIP) assay. Collectively, these methods provide a toolset that can expedite the development of aptamer ligands to target and deliver therapeutic siRNAs in vivo. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

  • 13.
    Hernandez, Frank J
    et al.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Hernandez, Luiza I.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Pinto, Alessandro
    NanoBioSeparations Group, POLYMAT, University of of the Basque Country UPV/EHU, Avda. Tolosa 72, Donostia-San-Sebastián, Spain.
    Schäfer, Thomas
    NanoBioSeparations Group, POLYMAT, University of of the Basque Country UPV/EHU, Avda. Tolosa 72, Donostia-San-Sebastián, Spain; Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain.
    Özalp, Veli C.
    Nanobiz Ltd. Metu Technopolis, 06800 Ankara, Turkey; Middle East Technical University, Biological Sciences, 06800 Ankara, Turkey.
    Targeting cancer cells with controlled release nanocapsules based on a single aptamer2013In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 49, no 13, p. 1285-1287Article in journal (Refereed)
    Abstract [en]

    Molecular gates have received considerable attention as drug delivery systems. More recently, aptamer-based gates showed great potential in overcoming major challenges associated with drug delivery by means of nanocapsules. Based on a switchable aptamer nanovalves approach, we herein report the first demonstration of an engineered single molecular gate that directs nanoparticles to cancer cells and subsequently delivers the payload in a controllable fashion. © 2012 The Royal Society of Chemistry.

  • 14.
    Hernandez, Frank J.
    et al.
    University of Iowa, Iowa City, USA.
    Botero Hincapié, Juliana Andrea
    Estudiante de Microbiología y Bioanálisis, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia..
    Aptámeros: agentes diagnósticos y terapéuticos2012In: Iatreia, ISSN 0121-0793, E-ISSN 2011-7965, Vol. 25, p. 159-168Article in journal (Refereed)
    Abstract [en]

    Aptamers are single-stranded DNA or RNA molecules that recognize a variety of target molecules with high levels of affinity and specificity, due to their particular three-dimensional structure. They are similar to antibodies regarding the recognition process. However, they offer significant advantages over antibodies based on their size, ease of production and various chemical modifications. Thus, they are excellent candidates for developing new biotechnological platforms. Up to date, several aptamers with therapeutic properties have been successfully evaluated in animal models and clinical trials. Moreover, one of them has already been approved by the FDA. Advances during the last two decades allow to foresee that aptamers will play a key role as diagnostic and therapeutic agents in the near future.

  • 15.
    Hernandez, Frank J
    et al.
    Department of Internal Medicine, Coralville, IA, United States.
    Stockdale, Katie R.
    Department of Internal Medicine, Coralville, IA, United States.
    Huang, Lingyan
    Integrated DNA Technologies, Inc., Coralville, IA, United States.
    Horswill, Alexander R.
    Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, 375 Newton Road, Iowa City, IA 52242, United States.
    Behlke, Mark A.
    Integrated DNA Technologies, Inc., Coralville, IA, United States.
    McNamara II, James O.
    Department of Internal Medicine, Coralville, IA, United States; Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, 375 Newton Road, Iowa City, IA 52242, United States.
    Degradation of nuclease-stabilized RNA oligonucleotides in Mycoplasma-contaminated cell culture media2012In: Nucleic Acid Therapeutics, ISSN 2159-3337, E-ISSN 2159-3345, Vol. 22, no 1, p. 58-68Article in journal (Refereed)
    Abstract [en]

    Artificial RNA reagents such as small interfering RNAs (siRNAs) and aptamers often must be chemically modified for optimal effectiveness in environments that include ribonucleases. Mycoplasmas are common bacterial contaminants of mammalian cell cultures that are known to produce ribonucleases. Here we describe the rapid degradation of nuclease-stabilized RNA oligonucleotides in a human embryonic kidney 293 (HEK) cell culture contaminated with Mycoplasma fermentans, a common species of mycoplasma. RNA with 2′-fluoro-or 2′-O-methyl-modified pyrimidines was readily degraded in conditioned media from this culture, but was stable in conditioned media from uncontaminated HEK cells. RNA completely modified with 2′-O-methyls was not degraded in the mycoplasma-contaminated media. RNA zymogram analysis of conditioned culture media and material centrifuged from the media revealed several distinct protein bands (ranging from 30 to 68kDa) capable of degrading RNA with 2′-fluoro-or 2′-O-methyl-modified pyrimidines. Finally, the mycoplasma-associated nuclease was detected in material centrifuged from the contaminated culture supernatants in as little as 15 minutes with an RNA oligo-containing 2′-O-methyl-modified pyrimidines and labeled with a 5′-fluorescein amidite (FAM) and 3′-quencher. These results suggest that mycoplasma contamination may be a critical confounding variable for cell culture experiments involving RNA-based reagents, with particular relevance for applications involving naked RNA (e.g., aptamer-siRNA chimeras). © 2012 Mary Ann Liebert, Inc.

  • 16.
    Thiel, Kristina W.
    et al.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Hernandez, Luiza I.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Dassie, Justin P.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; Department of Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA 52242, United States.
    Thiel, William H.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Liu, Xiuying
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Stockdale, Katie R.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Rothman, Alissa M.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Hernandez, Frank J
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    McNamara, James O.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States.
    Giangrande, Paloma H.
    Department of Internal Medicine, University of of Iowa, Iowa City, IA 52242, United States; Department of Radiation Oncology, University of of Iowa, Iowa City, IA 52242, United States.
    Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers2012In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no 13, p. 6319-6337Article in journal (Refereed)
    Abstract [en]

    Human epidermal growth factor receptor 2 (HER2) expression in breast cancer is associated with an aggressive phenotype and poor prognosis, making it an appealing therapeutic target. Trastuzumab, an HER2 antibody-based inhibitor, is currently the leading targeted treatment for HER2+-breast cancers. Unfortunately, many patients inevitably develop resistance to the therapy, highlighting the need for alternative targeted therapeutic options. In this study, we used a novel, cell-based selection approach for isolating cell-type specific, cell-internalizing RNA ligands (aptamers) capable of delivering therapeutic small interfering RNAs (siRNAs) to HER2-expressing breast cancer cells. RNA aptamers with the greatest specificity and internalization potential were covalently linked to siRNAs targeting the anti-apoptotic gene, Bcl-2. We demonstrate that, when applied to cells, the HER2 aptamer-Bcl-2 siRNA conjugates selectively internalize into HER2+-cells and silence Bcl-2 gene expression. Importantly, Bcl-2 silencing sensitizes these cells to chemotherapy (cisplatin) suggesting a potential new therapeutic approach for treating breast cancers with HER2+-status. In summary, we describe a novel cell-based selection methodology that enables the identification of cell-internalizing RNA aptamers for targeting therapeutic siRNAs to HER2-expressing breast cancer cells. The future refinement of this technology may promote the widespread use of RNA-based reagents for targeted therapeutic applications. © 2012 The Author(s).

  • 17.
    Hernandez, Frank J
    et al.
    Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 375 Newton Rd, Iowa City, IA 52242, USA.
    Ozalp, Veli Cengiz
    Institute for Polymer Materials (Polymat), University of the Basque Country, Avda. Tolosa 72, San Sebastian 20018, Spain.
    Graphene and other nanomaterial-based electrochemical aptasensors.2012In: Biosensors, ISSN 2079-6374, Vol. 2, no 1, p. 1-14Article in journal (Refereed)
    Abstract [en]

    Electrochemical aptasensors, which are based on the specificity of aptamer-target recognition, with electrochemical transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. Aptamers are functional nucleic acids with specific and high affinity to their targets, similar to antibodies. However, they are completely selected in vitro in contrast to antibodies. Due to their stability, easy chemical modifications and proneness to nanostructured device construction, aptamer-based sensors have been incorporated in a variety of applications including electrochemical sensing devices. In recent years, the performance of aptasensors has been augmented by incorporating novel nanomaterials in the preparation of better electrochemical sensors. In this review, we summarize the recent trends in the use of nanomaterials for developing electrochemical aptasensors.

  • 18.
    Huang, Yang Zhong
    et al.
    Department of Neurobiology, Duke University of Medical Center, Duke University, Durham, NC, United States.
    Hernandez, Frank J
    Department of Internal Medicine, University of of Iowa, MERF, 375 Newton Rd., Iowa City, IA 52242, United States.
    Gu, Bin
    Department of Pharmacology and Cancer Biology, Duke University of Medical Center, Duke University, Durham, NC, United States.
    Stockdale, Katie R.
    Department of Internal Medicine, University of of Iowa, MERF, 375 Newton Rd., Iowa City, IA 52242, United States.
    Nanapaneni, Kishore
    Center for Bioinformatics and Computational Biology, University of of Iowa, Iowa City, IA, United States; Department of Biomedical Engineering, University of of Iowa, Iowa City, IA, United States.
    Scheetz, Todd E.
    Center for Bioinformatics and Computational Biology, University of of Iowa, Iowa City, IA, United States; Department of Biomedical Engineering, University of of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, Roy J. and Lucille A. Carver College of Medicine, University of of Iowa, Iowa City, IA, United States.
    Behlke, Mark A.
    Integrated DNA Technologies, Coralville, IA, United States.
    Peek, Andrew S.
    Integrated DNA Technologies, Coralville, IA, United States.
    Bair, Thomas
    DNA Facility, University of of Iowa, Iowa City, IA, United States.
    Giangrande, Paloma H.
    Department of Internal Medicine, University of of Iowa, MERF, 375 Newton Rd., Iowa City, IA 52242, United States.
    McNamara, James O.
    Department of Internal Medicine, University of of Iowa, MERF, 375 Newton Rd., Iowa City, IA 52242, United States.
    RNA aptamer-based functional ligands of the neurotrophin receptor, TrkB2012In: Molecular Pharmacology, ISSN 0026-895X, E-ISSN 1521-0111, Vol. 82, no 4, p. 623-635Article in journal (Refereed)
    Abstract [en]

    Many cell surface signaling receptors, such as the neurotrophin receptor, TrkB, have emerged as potential therapeutic targets for diverse diseases. Reduced activation of TrkB in particular is thought to contribute to neurodegenerative diseases. Unfortunately, development of therapeutic reagents that selectively activate particular cell surface receptors such as TrkB has proven challenging. Like many cell surface signaling receptors, TrkB is internalized upon activation; in this proof-of-concept study, we exploited this fact to isolate a pool of nuclease-stabilized RNA aptamers enriched for TrkB agonists. One of the selected aptamers, C4-3, was characterized with recombinant protein-binding assays, cell-based signaling and functional assays, and, in vivo in a seizure model in mice. C4-3 binds the extracellular domain of TrkB with high affinity (KD ∼2 nM) and exhibits potent TrkB partial agonistic activity and neuroprotective effects in cultured cortical neurons. In mice, C4-3 activates TrkB upon infusion into the hippocampus; systemic administration of C4-3 potentiates kainic acid-induced seizure development. We conclude that C4-3 is a potentially useful therapeutic agent for neurodegenerative diseases in which reduced TrkB activation has been implicated. We anticipate that the cell-based aptamer selection approach used here will be broadly applicable to the identification of aptamer-based agonists for a variety of cell-surface signaling receptors. Copyright © 2012 The American Society for Pharmacology and Experimental Therapeutics.

  • 19.
    Pasternak, Anna
    et al.
    Nucleic Acid Center, Department of Physics and Chemistry, University of of Southern Denmark, 5230 Odense M, Denmark.
    Hernandez, Frank J
    Nucleic Acid Center, Department of Biochemistry and Molecular Biology, University of of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
    Rasmussen, Lars M.
    Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of of Southern Denmark, Sdr. Boulevard, 5000 Odense C, Denmark.
    Vester, Birte
    Nucleic Acid Center, Department of Biochemistry and Molecular Biology, University of of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
    Wengel, Jesper
    Nucleic Acid Center, Department of Physics and Chemistry, University of of Southern Denmark, 5230 Odense M, Denmark.
    Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer2011In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 39, no 3, p. 1155-1164Article in journal (Refereed)
    Abstract [en]

    A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA-U placed in position U3, U7 or U12 increases the thermodynamic stability of TBA by 0.15-0.50kcal/mol. In contrast, modification of any position within the two G-quartet structural elements is unfavorable for quadruplex formation. The intramolecular folding of the quadruplexes is confirmed by Tm versus ln c analysis. Moreover, circular dichroism and thermal difference spectra of the modified TBAs displaying high thermodynamic stability show bands that are characteristic for antiparallel quadruplex formation. Surface plasmon resonance studies of the binding of the UNA-modified TBAs to thrombin show that a UNA monomer is allowed in many positions of the aptamer without significantly changing the thrombin-binding properties. The biological effect of a selection of the modified aptamers was tested by a thrombin time assay and showed that most of the UNA-modified TBAs possess anticoagulant properties, and that the construct with a UNA-U monomer in position 7 is a highly potent inhibitor of fibrin-clot formation. © 2010 The Author(s).

  • 20.
    Rockey, William M.
    et al.
    Department of Radiation Oncology, University of of Iowa, Iowa City, IA, United States.
    Hernandez, Frank J
    Department of Internal Medicine, University of of Iowa, 285 Newton Road, Iowa City, IA 52242, United States.
    Huang, Sheng-You
    Departments of Physics and Astronomy, United States; Department of Biochemistry, University of of Missouri, Columbia, MO, United States; Dalton Cardiovascular Research Center, University of of Missouri, Columbia, MO, United States; Informatics Institute, University of of Missouri, Columbia, MO, United States.
    Cao, Song
    Departments of Physics and Astronomy, United States; Department of Biochemistry, University of of Missouri, Columbia, MO, United States; Informatics Institute, University of of Missouri, Columbia, MO, United States.
    Howell, Craig A.
    Department of Internal Medicine, University of of Iowa, 285 Newton Road, Iowa City, IA 52242, United States.
    Thomas, Gregory S.
    Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA, United States.
    Liu, Xiu Ying
    Department of Internal Medicine, University of of Iowa, 285 Newton Road, Iowa City, IA 52242, United States.
    Lapteva, Natalia
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States.
    Spencer, David M.
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States.
    McNamara II, James O.
    Department of Internal Medicine, University of of Iowa, 285 Newton Road, Iowa City, IA 52242, United States.
    Zou, Xiaoqin
    Departments of Physics and Astronomy, United States; Department of Biochemistry, University of of Missouri, Columbia, MO, United States; Dalton Cardiovascular Research Center, University of of Missouri, Columbia, MO, United States; Informatics Institute, University of of Missouri, Columbia, MO, United States.
    Chen, Shi-Jie
    Departments of Physics and Astronomy, United States; Department of Biochemistry, University of of Missouri, Columbia, MO, United States; Informatics Institute, University of of Missouri, Columbia, MO, United States.
    Giangrande, Paloma H.
    Department of Radiation Oncology, University of of Iowa, Iowa City, IA, United States; Department of Internal Medicine, University of of Iowa, 285 Newton Road, Iowa City, IA 52242, United States; Molecular and Cellular Biology Program, University of of Iowa, Iowa City, IA, United States.
    Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling2011In: Nucleic Acid Therapeutics, ISSN 2159-3337, E-ISSN 2159-3345, Vol. 21, no 5, p. 299-314Article in journal (Refereed)
    Abstract [en]

    RNA aptamers represent an emerging class of pharmaceuticals with great potential for targeted cancer diagnostics and therapy. Several RNA aptamers that bind cancer cell-surface antigens with high affinity and specificity have been described. However, their clinical potential has yet to be realized. A significant obstacle to the clinical adoption of RNA aptamers is the high cost of manufacturing long RNA sequences through chemical synthesis. Therapeutic aptamers are often truncated postselection by using a trial-and-error process, which is time consuming and inefficient. Here, we used a rational truncation approach guided by RNA structural prediction and protein/RNA docking algorithms that enabled us to substantially truncateA9, an RNA aptamer to prostate-specific membrane antigen (PSMA),with great potential for targeted therapeutics. This truncated PSMA aptamer (A9L; 41mer) retains binding activity, functionality, and is amenable to large-scale chemical synthesis for future clinical applications. In addition, the modeled RNA tertiary structure and protein/RNA docking predictions revealed key nucleotides within the aptamer critical for binding to PSMA and inhibiting its enzymatic activity. Finally, this work highlights the utility of existing RNA structural prediction and protein docking techniques that may be generally applicable to developing RNA aptamers optimized for therapeutic use. © 2011 Mary Ann Liebert, Inc.

  • 21.
    Hernandez, Frank J
    et al.
    Nucleic Acid Center, Biochemistry and Molecular Biology Department, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Kalra, Neerja
    Department of Physics and Chemistry, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Wengel, Jesper
    Department of Physics and Chemistry, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Vester, Birte
    Nucleic Acid Center, Biochemistry and Molecular Biology Department, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Aptamers as a model for functional evaluation of LNA and 2′-amino LNA2009In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1090-2120, Vol. 19, no 23, p. 6585-6587Article in journal (Refereed)
    Abstract [en]

    The affinity change upon incorporation of LNA and 2′-amino-LNA monomers into an avidin binding DNA aptamer is described. The kinetic profile of selected modified-aptamer was obtained by surface plasmon resonance experiments and compared with the profile of the parent unmodified DNA aptamer. We report significant improvement of avidin binding affinity by the incorporation of single LNA modifications into the aptamer, and successful incorporation of 2′-amino LNA as a novel monomer in aptamers with potential function as carrier unit for additional molecular entities. © 2009 Elsevier Ltd. All rights reserved.

  • 22.
    Hernandez, Frank Jeyson
    et al.
    Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Dondapati, Srujan Kumar
    Photonics and Optoelectronics Group, Physics Department and Center for Nanoscience CeNS, Ludwig-Maximilians-Universität München, Munich, Germany.
    Ozalp, V Cengiz
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Pinto, Alessandro
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    O'Sullivan, Ciara K
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Klar, Thomas A
    Institute of Physics and Institute of Micro and Nanotechnologies, Technical University of Ilmenau, Ilmenau, Germany.
    Katakis, Ioannis
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Label free optical sensor for Avidin based on single gold nanoparticles functionalized with aptamers2009In: Journal of Biophotonics, ISSN 1864-063X, E-ISSN 1864-0648, Vol. 2, no 4, p. 227-231Article in journal (Refereed)
    Abstract [en]

    Optical spectroscopy of a single gold nanoparticle, functionalized with an aptamer, is used to sense the specific binding of avidin. Herewith, the field of single noble metal nanoparticle biosensors is extended to the important field of aptamer based assays. The sensitivity of this initial, but not yet optimized apta-nano-sensor is in the range of 20 nM. Due to its nanoscopic size, this single nanoparticle based apta-sensor may be used in nanoscopic volumes such as in array type assays or even inside cells.

1 - 22 of 22
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