- MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Ian W Davis
Department of Biochemistry, Duke University, Durham, NC, USA
Nucleic Acids Res 35:W375-83. 2007
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...
- Development and current status of the CHARMM force field for nucleic acids
A D MacKerell
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N Pine Street, Baltimore, MD 21201, USA
Biopolymers 56:257-65. 2000
The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations...
- Plasmacytoid dendritic cells: sensing nucleic acids in viral infection and autoimmune diseases
Department of Immunology and Center of Cancer Immunology Research, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
Nat Rev Immunol 8:594-606. 2008
..This function of pDCs is linked to their expression of Toll-like receptor 7 (TLR7) and TLR9, which sense viral nucleic acids within the early endosomes...
- Human CD14dim monocytes patrol and sense nucleic acids and viruses via TLR7 and TLR8 receptors
U838 INSERM, Universite Paris Descartes, Paris, France
Immunity 33:375-86. 2010
..they selectively produced TNF-α, IL-1β, and CCL3 in response to viruses and immune complexes containing nucleic acids, via a proinflammatory TLR7-TLR 8-MyD88-MEK pathway...
- Isolation of phosphatidylethanolamine as a solitary cofactor for prion formation in the absence of nucleic acids
Nathan R Deleault
Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
Proc Natl Acad Sci U S A 109:8546-51. 2012
..Recent reconstitution studies indicate that nucleic acids are not required for the propagation of mouse prions in vitro, suggesting the existence of an alternative ..
- MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
Ian W Davis
Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
Nucleic Acids Res 32:W615-9. 2004
..a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes...
- The structures of quadruplex nucleic acids and their drug complexes
Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29 39 Brunswick Square, London WC1N 1AX, UK
Curr Opin Struct Biol 19:239-50. 2009
Quadruplex nucleic acids are four-stranded structures formed from short tracts of G-rich sequence associating together...
- Contamination of clinical specimens with MLV-encoding nucleic acids: implications for XMRV and other candidate human retroviruses
Robert A Smith
Department of Pathology, University of Washington, Seattle WA, USA
Retrovirology 7:112. 2010
..These findings raise important questions regarding the provenance of XMRV and its potential connection to human disease...
- Chemical vectors for gene delivery: a current review on polymers, peptides and lipids containing histidine or imidazole as nucleic acids carriers
Centre de Biophysique Moléculaire CNRS UPR 4301 affiliated to the University of Orléans and Inserm, rue Charles Sadron, F 45071 Orleans cedex 2, France
Br J Pharmacol 157:166-78. 2009
..and DNA/cationic polymer/cationic lipid (lipopolyplexes) electrostatic complexes are proposed as non-viral nucleic acids delivery systems...
- Nucleic acids within urinary exosomes/microvesicles are potential biomarkers for renal disease
Kevin C Miranda
Division of Nephrology, Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
Kidney Int 78:191-9. 2010
..We sought to identify whether these microvesicles contain nucleic acids. We isolated microvesicles from human urine in the same density range as that previously described for urinary ..
- Peptide vectors for the nonviral delivery of nucleic acids
Translational Centre for Regenerative Medicine, University of Leipzig, Germany
Acc Chem Res 45:1048-56. 2012
..However, the therapeutic applications of nucleic acids extend beyond the delivery of double-stranded DNA and subsequent expression of deficient gene products in ..
- Architecture and nucleic acids recognition mechanism of the THO complex, an mRNP assembly factor
Department of Structure of Macromolecules, Centro Nacional de Biotecnologia CNB CSIC, Madrid, Spain
EMBO J 31:1605-16. 2012
..Furthermore, we show that THO directly interacts with nucleic acids through the unfolded C-terminal region of Tho2, whose removal reduces THO recruitment to active chromatin ..
- Synthetic genetic polymers capable of heredity and evolution
Vitor B Pinheiro
Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Science 336:341-4. 2012
..from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]...
- Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes
Julian Leon Huppert
Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge, UKCB3 0HE
Chem Soc Rev 37:1375-84. 2008
There are many structures that can be adopted by nucleic acids other than the famous Watson-Crick duplex form...
- Point-of-care nucleic acid testing for infectious diseases
Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
Trends Biotechnol 29:240-50. 2011
..It briefly discusses selected applications related to the diagnosis and management of tuberculosis, HIV, and perinatal and nosocomial infections...
- Specific localisation of human cytomegalovirus nucleic acids and proteins in human colorectal cancer
Pathology Service, Birmingham Veterans Affairs Hospital, Birmingham, AL, USA
Lancet 360:1557-63. 2002
..We aimed to assess whether gene products of human cytomegalovirus could be detected in colorectal cancers...
- Therapeutic applications of nucleic acids and their analogues in Toll-like receptor signaling
Department of Molecular Science and Technology, Ajou University, Suwon 443 749, Korea
Molecules 17:13503-29. 2012
..Specifically intracellular TLRs such as TLR3, TLR7, TLR8 and TLR9 recognize nucleic acids such as double-stranded RNA, single-stranded RNA and CpG DNA respectively derived from microbial components...
- Oxidative damage to nucleic acids photosensitized by titanium dioxide
W G Wamer
Center for Food Safety and Applied Nutrition, U S Food and Drug Administration, Washington, DC 20204, USA
Free Radic Biol Med 23:851-8. 1997
..However, no oxidative damage was detectable in cellular DNA. These results suggest that nucleic acids are a potential target for photooxidative damage sensitized by TiO2, and support the view that TiO2 ..
- Screening for circulating nucleic acids and caspase activity in the peripheral blood as potential diagnostic tools in lung cancer
Institute of Tumor Biology, University Medical Center Hamburg Eppendorf, Germany
Mol Oncol 5:281-91. 2011
The focus of the current investigational study was to examine whether circulating nucleic acids (i.e., DNA and microRNAs) have the potential to become suitable blood-based markers for diagnosis and progression of lung cancer...
- TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus
Dynavax Technologies Corporation, 2929 Seventh Street, Suite 100, Berkeley, California 94710, USA
Nature 465:937-41. 2010
..Recognition of self nucleic acids by toll-like receptors TLR7 and TLR9 on B cells and plasmacytoid dendritic cells (PDCs) is an important step ..
- Autoimmune skin inflammation is dependent on plasmacytoid dendritic cell activation by nucleic acids via TLR7 and TLR9
Dynavax Technologies Corporation, Berkeley, CA 94710, USA
J Exp Med 207:2931-42. 2010
..These data suggest that inhibitors of TLR7 and TLR9 signaling have potential therapeutic application for the treatment of interface dermatitis...
- Recognition of nucleic acids by pattern-recognition receptors and its relevance in autoimmunity
Laboratory of Host Defense, WPI Immunology Frontier Research Center, Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
Immunol Rev 243:61-73. 2011
..b>Nucleic acids, which are critical components for inheriting genetic information in all species including pathogens, are key ..
- Vitamin B12-derivatives-enzyme cofactors and ligands of proteins and nucleic acids
Institute of Molecular Biosciences, University of Graz, Humboldtstr 50 3, Graz, A 8010, Austria
Chem Soc Rev 40:4346-63. 2011
- Relevance of circulating tumor cells, extracellular nucleic acids, and exosomes in breast cancer
Anne M Friel
School of Pharmacy and Pharmaceutical Sciences and Molecular Therapeutics for Cancer Ireland, Trinity College Dublin, Dublin 2, Ireland
Breast Cancer Res Treat 123:613-25. 2010
..Circulating tumor cells and extracellular nucleic acids have been detected within blood, plasma, and sera of cancer patients...
- Predicting secondary structural folding kinetics for nucleic acids
Department of Physics, Wuhan University, Wuhan, China
Biophys J 98:1617-25. 2010
..The approach presented here may provide a robust first step for further systematic development of a predictive theory for the folding kinetics for large RNAs...
- Microparticle-associated nucleic acids mediate trait dominance in cancer
Sydney Medical School and Bosch Institute, University of Sydney, Sydney, Australia
FASEB J 26:420-9. 2012
..We show that MDR MPs incorporate nucleic acids; MPs change recipient cells' transcriptional environment to reflect donor MDR phenotype, and distinct pathways ..
- Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue
Stephen M Hewitt
Tissue Array Research Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4605, USA
Arch Pathol Lab Med 132:1929-35. 2008
..Limiting the utility of expression profiling is the isolation of quality nucleic acids from formalin-fixed, paraffin-embedded tissue...
- Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family
Systèmes moléculaires et Biologie structurale, LMCP, CNRS UMR 7590, Universités Paris 6 et Paris 7, case 115, 4 place Jussieu, F 75252 Paris Cedex 05, France
Nucleic Acids Res 30:3592-601. 2002
- Chitosans for delivery of nucleic acids
Michael D Buschmann
Dept Chemical Engineering and Inst Biomedical Engineering, Ecole Polytechnique, Montreal, QC, Canada Electronic address
Adv Drug Deliv Rev 65:1234-70. 2013
..In each, we present the obstacles to efficient transfection and the strategies adopted over time to surmount these impediments. ..
- Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids
Direction des Sciences de Matière, Institut Nanosciences et Cryogenie, CEA Grenoble, Grenoble Cedex 9, France
Free Radic Res 46:367-81. 2012
..aimed at delineating the mechanisms of formation and cellular processing of oxidatively generated damage to nucleic acids. Perhaps as a consequence of this breadth of research expertise, there are nomenclature problems for several ..
- DNA polymerase-mediated DNA synthesis on a TNA template
John C Chaput
Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
J Am Chem Soc 125:856-7. 2003
..We report that despite having a repeating unit that is one atom shorter than that of DNA, several polymerases showed surprisingly good ability to copy limited stretches of TNA...
- Two sides of the coin: affinity and specificity of nucleic acid interactions
Vadim V Demidov
Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
Trends Biochem Sci 29:62-71. 2004
..recent progress in understanding the molecular mechanisms of nucleic acid interactions and the development of new high-affinity plus high-specificity oligonucleotides and their mimics, with particular emphasis on peptide nucleic acids.
- The polyethyleneglycol dilemma: advantage and disadvantage of PEGylation of liposomes for systemic genes and nucleic acids delivery to tumors
Laboratory of Innovative Nanomedicine, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
Biol Pharm Bull 36:892-9. 2013
..Then, endosomal fusogenic peptides are discussed. Finally, pH-sensitive liposomes using pH-sensitive lipids are described...
- Crystal growth of proteins, nucleic acids, and viruses in gels
Architecture et Reactivite de l ARN, Universite de Strasbourg, CNRS, IBMC, 15 rue Rene Descartes, 67084 Strasbourg, France
Prog Biophys Mol Biol 101:13-25. 2009
..Methods and techniques implemented with proteins can also be applied to nucleic acids and nucleoprotein assemblies such as viruses.
- Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2'-C-piperazino-UNA monomer
Troels B Jensen
Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
Bioorg Med Chem 19:4739-45. 2011
..Most of the studied variants bind thrombin, albeit with decreased affinity in reference to unmodified TBA. Thrombin time assay studies indicate three variants as being as potent as TBA in fibrin clotting inhibition...
- Modeling nucleic acids
Adelene Y L Sim
Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
Curr Opin Struct Biol 22:273-8. 2012
b>Nucleic acids are an important class of biological macromolecules that carry out a variety of cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold into precise three-dimensional structures...
- Efficient and rapid template-directed nucleic acid copying using 2'-amino-2',3'-dideoxyribonucleoside-5'-phosphorimidazolide monomers
Jason P Schrum
Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Harvard Medical School, Boston, Massachusetts 02114, USA
J Am Chem Soc 131:14560-70. 2009
- A library of IR bands of nucleic acids in solution
Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, S 106 91, Stockholm, Sweden
Biophys Chem 104:477-88. 2003
This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations...
- Point detection of pathogens in oral samples
University of Pennsylvania School of Dental Medicine, 240 South 40th Street, Philadelphia, PA 19104 6030, USA
Adv Dent Res 18:12-6. 2005
- Circulating nucleic acids and critical illness
Timothy H Rainer
Accident and Emergency Medicine Academic Unit, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR
Ann N Y Acad Sci 1075:271-7. 2006
..reviews some of the early work that has been performed to investigate the potential roles of circulating nucleic acids as prediction markers in acute illness and injury...
- A binary DNA probe for highly specific nucleic Acid recognition
Dmitry M Kolpashchikov
Division of Experimental Therapeutics, Department of Medicine, Columbia University, Box 84, 630W 168th Street, New York, New York 10032, USA
J Am Chem Soc 128:10625-8. 2006
..5% of the analyte in excess amount of a single base substituted oligodeoxyribonucleotide and distinguishes single nucleotide substitutions at any position of a 20-mer oligonucleotide at room temperature...
- Intracellular nucleic acid sensors and autoimmunity
Argyrios N Theofilopoulos
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92137, USA
J Interferon Cytokine Res 31:867-86. 2011
..if the molecular signatures recognized are shared by both foreign and self-molecules, as is the case of nucleic acids, then the responses initiated by these sensors may have deleterious consequences...
- Preparation and evaluation of packed capillary columns for the separation of nucleic acids by ion-pair reversed-phase high-performance liquid chromatography
Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck. Austria
J Chromatogr A 893:23-35. 2000
- Electrochemical simulation of oxidation processes involving nucleic acids monitored with electrospray ionization-mass spectrometry
Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
Anal Bioanal Chem 397:1203-15. 2010
Oxidation is commonly involved in the alteration of nucleic acids giving rise to diverse effects including mutation, cell death, malignancy, and aging...
- Oxidative damage to nucleic acids in severe emphysema
Washington University School of Medicine, Division of Pulmonary and Critical Care Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
Chest 135:965-74. 2009
Oxidative stress is a key element in the pathogenesis of emphysema, but oxidation of nucleic acids has been largely overlooked. The aim of this study was to investigate oxidative damage to nucleic acids in severe emphysematous lungs.
- Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication
FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
J Am Chem Soc 132:5880-5. 2010
..Our study suggests that the emergence of functional sequences during the origin of life would be possible even in the face of the high intrinsic error rates of chemical replication...
- 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
Xiang Jun Lu
Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854 8087, USA
Nat Protoc 3:1213-27. 2008
..The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/...
- Multicentre validation study of nucleic acids extraction from FFPE tissues
ACADEM Department University of Trieste and ICGEB, University of Trieste, Cattinara Hospital, 34149 Trieste, Italy
Virchows Arch 457:309-17. 2010
..Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, ..
- Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
Ted A Laurence
Physical Biosciences Institute, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Proc Natl Acad Sci U S A 102:17348-53. 2005
..We propose that the larger fluctuations may indicate transient residual structure in the unfolded state...
- Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba
Centre for Biomolecular Sciences, University of St Andrews, Fife KY169ST, U K
Biochem J 427:49-55. 2010
..Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer-dimer interaction forms in the presence of dsDNA...
- Nonviral approaches for neuronal delivery of nucleic acids
Jamie M Bergen
Bioengineering, University of Washington, Seattle, WA 98195, USA
Pharm Res 25:983-98. 2008
The delivery of therapeutic nucleic acids to neurons has the potential to treat neurological disease and spinal cord injury...
- Enzymatic incorporation of LNA nucleotides into DNA strands
Rakesh N Veedu
Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
Chembiochem 8:490-2. 2007
- Circulating nucleic acids in plasma or serum (CNAPS) as prognostic and predictive markers in patients with solid neoplasias
Department of Medical Statistics, Informatics and Health Economics, Innsbruck Medical University, A 6020 Innsbruck, Austria
Dis Markers 21:105-20. 2005
..Approximately a decade ago tumor-derived circulating nucleic acids in the plasma or serum (CNAPS) of cancer patients were introduced as a noninvasive tool for cancer detection...
- Inorganic nanoparticles as carriers of nucleic acids into cells
Institut fur Anorganische Chemie, Universitat Duisburg Essen, Universitätsstrasse 5 7, 45117 Essen, Germany
Angew Chem Int Ed Engl 47:1382-95. 2008
The transfer of nucleic acids (DNA or RNA) into living cells, that is, transfection, is a major technique in current biochemistry and molecular biology...
- Liposomes and virosomes as delivery systems for antigens, nucleic acids and drugs
Berna Biotech Ltd, Rehhagstrasse 79, CH 3018, Berne, Switzerland
Curr Opin Biotechnol 15:518-29. 2004
- Isolation and characterization of low nucleic acid (LNA)-content bacteria
Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, Switzerland
ISME J 3:889-902. 2009
..Their isolation and cultivation allow further detailed investigation of this group of organisms under defined laboratory conditions...
- Nucleic acids electrotransfer-based gene therapy (electrogenetherapy): past, current, and future
L M Mir
Centre National de la Recherche Scientifique, UMR 8121, Institut Gustave Roussy, 39 Rue C Desmoulins, Villejuif Cedex, France
Mol Biotechnol 43:167-76. 2009
..This knowledge has allowed developing new nucleic acids electrotransfer conditions using combinations of permeabilizing pulses of high voltage and short duration, and ..
- Effect of fixatives and tissue processing on the content and integrity of nucleic acids
Department of Pathology, Tzagournis Medical Research Facility, The Ohio State University, 420 West 12th Avenue, Columbus, OH 43210, USA
Am J Pathol 161:1961-71. 2002
..In addition, the parameters of procurement and fixation that affect the quality of the tissues at the molecular level are discussed...
- Electrically-assisted nucleic acids delivery to tissues in vivo: where do we stand?
IPBS CNRS, UMR 5089, 205, route de Narbonne, 31077 Toulouse Cedex, France
Curr Pharm Des 12:3817-25. 2006
..In the long run, this review should encourage other scientists to consider electrically assisted gene delivery for gene therapy as it matures...
- Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems?
Observatoire Oceanologique, Universite Pierre et Marie Curie, UMR 7621 7628 CNRS INSU, 66651 Banyuls sur Mer Cedex, France
Appl Environ Microbiol 67:1775-82. 2001
- Characterization of synthetic nucleic acids by electrospray ionization quadrupole time-of-flight mass spectrometry
Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
J Mass Spectrom 40:932-45. 2005
..quadrupole-quadrupole-time-of-flight mass spectrometry (ESI-QqTOF-MS) for the characterization of synthetic nucleic acids was evaluated...
- Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological molecules
W Russ Algar
Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd North, Mississauga, ON, L5L 1C6, Canada
Anal Bioanal Chem 391:1609-18. 2008
..Researchers have used QDs as energy donors in FRET schemes for the analysis of nucleic acids, proteins, proteases, haptens, and other small molecules. This paper reviews these applications of QDs...
- Cell-free nucleic acids as potential markers for preeclampsia
Laboratory for Prenatal Medicine, Department of Biomedicine, University Hospital, Spitalstrasse 21, CH 4031 Basel, Switzerland
Placenta 32:S17-20. 2011
..Circulating cell-free nucleic acids in plasma and serum are novel biomarkers with promising clinical applications in different medical fields, ..
- Innate immunity in systemic lupus erythematosus: sensing endogenous nucleic acids
Rheumatology, Clinical Immunology and Allergy, Graduate Program Molecular Basis of Human Diseases, University of Crete, Greece
J Autoimmun 35:206-11. 2010
..According to the current paradigm, nucleosomes containing nucleic acids (RNA and/or DNA) and other endogenous danger ligands that can bind to pathogen associated molecular pattern ..
- Role of the unstructured N-terminal domain of the hAPE1 (human apurinic/apyrimidinic endonuclease 1) in the modulation of its interaction with nucleic acids and NPM1 (nucleophosmin)
Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
Biochem J 452:545-57. 2013
..In the present study, we characterized the requirements for the interaction of hAPE1 with NPM1 and undamaged nucleic acids. We show that DNA/RNA secondary structure has an impact on hAPE1 binding in the absence of damage...
- Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity
Simon G Trevino
Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02144, USA
Proc Natl Acad Sci U S A 108:13492-7. 2011
..this possibility in a simplified model system, by using a T7 RNA polymerase variant capable of transcribing nucleic acids that contain an approximately 11 mixture of deoxy- and ribonucleotides...
- Circulating nucleic acids in plasma/serum
Jason C H Tsang
Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR
Pathology 39:197-207. 2007
Since the discovery of circulating nucleic acids in plasma in 1948, many diagnostic applications have emerged...
- Lipid nanoparticles as vehicles for macromolecules: nucleic acids and peptides
Ana del Pozo-Rodríguez
University of the Basque Country, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Paseo de la Universidad, 7 01006 Vitoria Gasteiz, Spain
Recent Pat Drug Deliv Formul 5:214-26. 2011
..Moreover, in the case of nucleic acids strategies to improve transfection mediated by lipid nanoparticles (entrance to the cells, intracellular ..
- How cationic lipids transfer nucleic acids into cells and across cellular membranes: recent advances
Zia ur Rehman
University Medical Center Groningen, University of Groningen, Department of Cell Biology, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
J Control Release 166:46-56. 2013
..polymer-based nanodevices are considered appropriate alternatives for virus-based particles for delivery of nucleic acids, including genes and siRNA, into eukaryotic cells...
- A rapid assay for affinity and kinetics of molecular interactions with nucleic acids
Gregory P Donaldson
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 40:e48. 2012
..Sequestration of biotinylated nucleic acids by streptavidin allowed nucleic acids to take the place of the protein as the immobile binding partner...
- Development of a generic microfluidic device for simultaneous detection of antibodies and nucleic acids in oral fluids
Rheonix, Inc, Ithaca, NY 14850, USA
Biomed Res Int 2013:543294. 2013
..The serological result is available in less than 30 min, and the confirmation by RNA amplification takes another 60 min. This approach combines a core serological portable diagnostic with a nucleic acid-based confirmatory test...
- Cell-penetrating peptides for the delivery of nucleic acids
University of Tartu, Institute of Technology, Laboratory of Molecular Biotechnology, Tartu, Estonia
Expert Opin Drug Deliv 9:823-36. 2012
..Recently, non-viral delivery of nucleic acids and their analogs has gained significant interest...
- NMR methodology for the study of nucleic acids
National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
Curr Opin Struct Biol 11:275-81. 2001
During the past few years, NMR methodology for the study of nucleic acids has benefited from new developments that greatly improved state-of-the-art technology for the precise determination of three-dimensional structures...
- Prediction of interactiveness of proteins and nucleic acids based on feature selections
Chemical Data mining Laboratory, Department of Chemistry, College of Sciences, Shanghai University, 99 Shang Da Road, Shanghai, 200444, People s Republic of China
Mol Divers 14:627-33. 2010
It is important to identify which proteins can interact with nucleic acids for the purpose of protein annotation, since interactions between nucleic acids and proteins involve in numerous cellular processes such as replication, ..
- MELTING, a flexible platform to predict the melting temperatures of nucleic acids
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
BMC Bioinformatics 13:101. 2012
..MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids. MELTING 4...
- Fixation of brain tumor biopsy specimens with RCL2 results in well-preserved histomorphology, immunohistochemistry and nucleic acids
Department of Medicine I, Medical University of Vienna, Vienna, Austria
Brain Pathol 20:1010-20. 2010
RCL2 is an alcohol-based fixative reported to preserve histomorphology and nucleic acids in non-CNS neoplasms...
- Analytical ancestry: "firsts" in fluorescent labeling of nucleosides, nucleotides, and nucleic acids
Larry J Kricka
Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Clin Chem 55:670-83. 2009
The inherent fluorescent properties of nucleosides, nucleotides, and nucleic acids are limited, and thus the need has arisen for fluorescent labeling of these molecules for a variety of analytical applications.
- PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids
Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Campus de Montegacedo S N, Boadilla del Monte, Madrid, Spain
Bioinformatics 26:2801-2. 2010
..Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them...
- Microfluidic sample preparation: cell lysis and nucleic acid purification
Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
Integr Biol (Camb) 1:574-86. 2009
..We classify the nucleic acid purification techniques according to the mechanism that links nucleic acids to substrates: silica-based surface affinity, electrostatic interaction, nanoporous membrane filtration, and ..
- Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes
Swiss Federal Institute of Aquatic Science and Technology EAWAG, P O Box 611, Uberlandstr 133, CH 8600 Dubendorf, Switzerland
Water Res 42:269-77. 2008
..We have shown that total cell concentration measured with FCM is a rapid, easy, sensitive and importantly, a descriptive parameter of several widely applied drinking water treatment processes...
- Analysis of human immunodeficiency virus type 1 matrix binding to membranes and nucleic acids
Department of Microbiology, Vollum Institute, Oregon Health and Science University, Portland, Oregon 97201 3098, USA
J Virol 83:12196-203. 2009
..MA also binds nucleic acids, although the significance of this association with regard to the viral life cycle is unclear...
- Bioresponsive polymers for the delivery of therapeutic nucleic acids
Pharmaceutical Biotechnology, LMU University, Butenandtstrasse 5 13, Munich, Germany
Wiley Interdiscip Rev Nanomed Nanobiotechnol 3:33-46. 2011
Polymers present an interesting option for the delivery of genes and other therapeutic nucleic acids. In the delivery process, the polymeric carriers face many different delivery tasks and different physiological microenvironments...
- High detection rates of nucleic acids of a wide range of respiratory viruses in the nasopharynx and the middle ear of children with a history of recurrent acute otitis media
Selma P Wiertsema
School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
J Med Virol 83:2008-17. 2011
..In this study molecular methods were used to determine the presence of nucleic acids of human rhinoviruses (HRV; types A, B, and C), respiratory syncytial viruses (RSV; types A and B), bocavirus (..
- A sensitive two-color electrophoretic mobility shift assay for detecting both nucleic acids and protein in gels
Proteomics Section, Molecular Probes Inc, 29851 Willow Creek Road, Eugene, OR 97402, USA
Proteomics 3:1172-80. 2003
..b>Nucleic acids are detected with SYBR Green EMSA dye, while proteins are subsequently detected with SYPRO Ruby EMSA dye...
- Reference ranges of urinary biomarkers of oxidized guanine in (2'-deoxy)ribonucleotides and nucleic acids
Laboratory of Industrial Toxicology, Department of Clinical Medicine, Nephrology, and Health Sciences, ISPESL National Institute for Occupational Safety and Prevention, Research Center, University of Parma, Parma, Italy
Free Radic Biol Med 50:254-61. 2011
..was aimed at defining the reference ranges for biomarkers of oxidized guanine in (2'-deoxy)ribonucleotides and nucleic acids from a large Italian sample. We recruited 300 healthy subjects (150 males; mean age 44.1±13...
- Circulating nucleic acids in cancer and pregnancy
Department of Clinical Physiopathology, University of Florence and Istituto Toscano Tumori, Viale Pieraccini 6, 50139 Florence, Italy
Methods 50:302-7. 2010
Circulating nucleic acids are present in the blood of humans and other vertebrates...
- Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens
Division of Blood Disorders, National Center for Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
J Virol Methods 171:195-9. 2011
..study compared six automated nucleic acid extraction systems and one manual kit for their ability to recover nucleic acids from human nasal wash specimens spiked with five respiratory pathogens, representing Gram-positive bacteria (..
- Preparation and characterization of monodisperse core-shell Fe3O4@SiO2 microspheres and its application for magnetic separation of nucleic acids from E. coli BL21
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Nanjing 210096, PR China
J Biomed Nanotechnol 8:1000-5. 2012
..And then, the prepared monodisperse core-shell Fe3O4@SiO2 microspheres were subsequently applied to separate nucleic acids from the bacteria (E...
- Thermoplastic microfluidic device for on-chip purification of nucleic acids for disposable diagnostics
Department of Biomedical Engineering, Boston University, Massachusetts 02215, USA
Anal Chem 78:788-92. 2006
A polymeric microfluidic device for solid-phase extraction (SPE)-based isolation of nucleic acids is demonstrated...
- Method for detection of specific nucleic acids by recombinant protein with fluorescent resonance energy transfer
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama, 226 8501, Japan
Anal Chem 77:4308-14. 2005
Detection of specific nucleic acids is important to understand cellular mechanisms and functions of gene regulation. Here, we demonstrated a novel method to detect specific nucleic acids using recombinant protein and oligonucleotides...
- Archaeal nucleic acids in picoplankton from great lakes on three continents
B P Keough
University of Minnesota Duluth, Duluth, MN, USA
Microb Ecol 46:238-48. 2003
..Despite their abundance in the water column of freshwater lakes, we have no representatives of these crenarchaea in pure culture, and so their physiological characteristics and ecological role remain unknown...
- Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins
Gerard C L Wong
Materials Science and Engineering Department, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Annu Rev Phys Chem 61:171-89. 2010
..Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states...
- Cationic polymer based nanocarriers for delivery of therapeutic nucleic acids
Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, Montreal, Quebec, Canada H2W 1R7
J Biomed Nanotechnol 7:504-20. 2011
The design and development of nucleic acids based therapeutics for the treatment of diseases arising from genetic abnormalities has made significant progress over the past few years...
- Characterization of nucleic acids by nanopore analysis
David W Deamer
Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
Acc Chem Res 35:817-25. 2002
..As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade...
- Electrostatic-assembly-driven formation of supramolecular rhombus microparticles and their application for fluorescent nucleic acid detection
State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
PLoS ONE 6:e18958. 2011
..In the following assay, specific hybridization with its target to form double-stranded DNA (dsDNA) results in desorption of ssDNA from SRM surface and subsequent fluorescence recovery...
- Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipids
Universite Victor Segalen, Bordeaux, F 33076, France
Org Biomol Chem 6:1324-33. 2008
..This Perspective highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology...
- Circular dichroism spectroscopic studies reveal pH dependent binding of curcumin in the minor groove of natural and synthetic nucleic acids
Institute of Biomolecular Chemistry, Chemical Research Center, H 1525, Budapest, P O Box 17, Hungary
Org Biomol Chem 2:2902-10. 2004
..As well as being an essentially new phenolic minor groove binder agent curcumin is also a promising molecular probe to study biologically important, pH and cation induced conformational polymorphisms of nucleic acids.
- Intraneuronal amyloid beta accumulation and oxidative damage to nucleic acids in Alzheimer disease
Department of Neuropsychiatry, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409 3898, Japan
Neurobiol Dis 37:731-7. 2010
..disease, we used an in situ approach to identify amyloid-beta (Abeta) accumulation and oxidative damage to nucleic acids in postmortem brain tissue of the hippocampal formation from subjects with Alzheimer disease...
- Pyrene excimer signaling molecular beacons for probing nucleic acids
Center for Research at Bio nano Interface, Department of Chemistry and Shands Cancer Center, University of Florida Genetics Institute, University of Florida, Gainesville, Florida 32611 7200, USA
J Am Chem Soc 130:336-42. 2008
..The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes...
- Fetal nucleic acids in maternal body fluids: an update
Diana W Bianchi
Tufts New England Medical Center, Box 394, 750 Washington Street, Boston, MA 02111, USA
Ann N Y Acad Sci 1075:63-73. 2006
..On the other hand, we are cautious and concerned about the accuracy of "at-home" kits for fetal gender detection...
- Delivery of nucleic acids with a stearylated (RxR)4 peptide using a non-covalent co-incubation strategy
Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
J Control Release 141:42-51. 2010
..These features make this stearic acid modified analog of (RxR)(4) an intriguing vector for future in vivo experiments...