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| nucleic acidsSummarySummary: High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages. Top Publications
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Publications
MolProbity: all-atom contacts and structure validation for proteins and nucleic acidsIan W Davis
Department of Biochemistry, Duke University, Durham, NC, USA
Nucleic Acids Res 35:W375-83. 2007MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...- Contamination of clinical specimens with MLV-encoding nucleic acids: implications for XMRV and other candidate human retrovirusesRobert 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... 
Development and current status of the CHARMM force field for nucleic acidsA D MacKerell
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N Pine Street, Baltimore, MD 21201, USA
Biopolymers 56:257-65. 2000The 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 diseasesMichel Gilliet
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 receptorsJerome Cros
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... - Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissueStephen 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... - The structures of quadruplex nucleic acids and their drug complexesStephen Neidle
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. 2009Quadruplex nucleic acids are four-stranded structures formed from short tracts of G-rich sequence associating together... - Four-stranded nucleic acids: structure, function and targeting of G-quadruplexesJulian Leon Huppert
Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge, UKCB3 0HE
Chem Soc Rev 37:1375-84. 2008There are many structures that can be adopted by nucleic acids other than the famous Watson-Crick duplex form... - Specific localisation of human cytomegalovirus nucleic acids and proteins in human colorectal cancerLualhati Harkins
Pathology Service, Birmingham Veterans Affairs Hospital, Birmingham, AL, USA
Lancet 360:1557-63. 2002..To detect human cytomegalovirus proteins and nucleic acids, we used immunohistochemistry with two different monoclonal antibodies, in-situ hybridisation, and PCR with .. - Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein AlbaClare Jelinska
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 acidsJamie M Bergen
Bioengineering, University of Washington, Seattle, WA 98195, USA
Pharm Res 25:983-98. 2008The delivery of therapeutic nucleic acids to neurons has the potential to treat neurological disease and spinal cord injury... - Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replicationSudha Rajamani
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... - Screening for circulating nucleic acids and caspase activity in the peripheral blood as potential diagnostic tools in lung cancerCarina Roth
Institute of Tumor Biology, University Medical Center Hamburg Eppendorf, Germany
Mol Oncol 5:281-91. 2011The 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... - Oxidative damage to nucleic acids in severe emphysemaGaetan Deslee
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. 2009Oxidative 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. - Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological moleculesW 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... - MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexesIan 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... - Multicentre validation study of nucleic acids extraction from FFPE tissuesSerena Bonin
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, .. - Liposomes and virosomes as delivery systems for antigens, nucleic acids and drugsDiana Felnerova
Berna Biotech Ltd, Rehhagstrasse 79, CH 3018, Berne, Switzerland
Curr Opin Biotechnol 15:518-29. 2004.... - Cationic polymer based nanocarriers for delivery of therapeutic nucleic acidsSurendra Nimesh
Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, Montreal, Quebec, Canada H2W 1R7
J Biomed Nanotechnol 7:504-20. 2011The 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... - Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipidsArnaud Gissot
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 acidsFerenc Zsila
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 diseaseAkihiko Nunomura
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... - Characterization of nucleic acids by nanopore analysisDavid 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 detectionHailong Li
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... - Inorganic nanoparticles as carriers of nucleic acids into cellsViktoriya Sokolova
Institut fur Anorganische Chemie, Universitat Duisburg Essen, Universitätsstrasse 5 7, 45117 Essen, Germany
Angew Chem Int Ed Engl 47:1382-95. 2008The transfer of nucleic acids (DNA or RNA) into living cells, that is, transfection, is a major technique in current biochemistry and molecular biology... - Nucleic acids electrotransfer-based gene therapy (electrogenetherapy): past, current, and futureL 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 .. - Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteinsGerard 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... - Cell-free nucleic acids as potential markers for preeclampsiaS Hahn
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, .. - Cationic gold microparticles for biolistic delivery of nucleic acidsSergei Svarovsky
Center for Innovations in Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA
Biotechniques 45:535-40. 2008..Along with its superior properties as a DNA delivery vehicle, charge-modified gold offers a unique opportunity to deliver various DNA formulations in addition to traditional naked DNA... - Fetal nucleic acids in maternal body fluids: an updateDiana 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... - Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopyAlexandar L Hansen
Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
J Am Chem Soc 131:3818-9. 2009..weak radiofrequency fields and selective polarization transfers for quantifying chemical-exchange processes in nucleic acids. The experiment extends the range of accessible time scales to approximately 10 ms, and its time-saving .. - Delivery of nucleic acids with a stearylated (RxR)4 peptide using a non-covalent co-incubation strategyTaavi Lehto
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... - Pyrene excimer signaling molecular beacons for probing nucleic acidsPatrick Conlon
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... - Autoimmune skin inflammation is dependent on plasmacytoid dendritic cell activation by nucleic acids via TLR7 and TLR9Cristiana Guiducci
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... - Delivery of proteins and nucleic acids using a non-covalent peptide-based strategySebastien Deshayes
Centre de Recherches de Biochimie Macromoleculaire, CRBM CNRS, UMR5237, Department of Molecular Biophysics and Therapeutics, 1919 Route de Mende, 34293 Montpellier, France
Adv Drug Deliv Rev 60:537-47. 2008..Pep and MPG are short amphipathic peptides, which form stable nanoparticles with proteins and nucleic acids respectively... - Real-time genotyping with oligonucleotide probes containing locked nucleic acidsLuis A Ugozzoli
Bio Rad Laboratories, 2000 A Nobel Drive, Hercules, CA 94547, USA
Anal Biochem 324:143-52. 2004.... - Enzymatic incorporation of LNA nucleotides into DNA strandsRakesh 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 - Study on the interaction between silver nanoparticles and nucleic acids in the presence of cetyltrimethylammonium bromide and its analytical applicationJinHua Zheng
Key Laboratory of Colloid and Interface Chemistry Shandong University, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, PR China
Talanta 74:526-32. 2008..bromide (CTMAB) is used as the probe of resonance light scattering (RLS) for the determination of nucleic acids. Under optimum conditions, there are linear relationships between the quenching extent of RLS and the .. - Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and SurflexPatrick A Holt
James Graham Brown Cancer Center and the Department of Medicine, University of Louisville, 5239 S Jackson Street, Louisville, KY 40202, USA
J Chem Inf Model 48:1602-15. 2008..the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove .. - Circulating nucleic acids in plasma or serum (CNAPS) as prognostic and predictive markers in patients with solid neoplasiasGeorg Goebel
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... - Analysis of human immunodeficiency virus type 1 matrix binding to membranes and nucleic acidsAyna Alfadhli
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... - MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate dataWilliam J Salerno
Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3500, USA
Nucleic Acids Res 32:W566-8. 2004..Potential applications of Monster range from mining and validating experimentally determined structures to guiding functional analysis. Non-commercial users can perform Monster analysis free of charge at http://monster.northwestern.edu... - BioMagResBankEldon L Ulrich
Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
Nucleic Acids Res 36:D402-8. 2008..consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and .. - Prenatal diagnosis: progress through plasma nucleic acidsY M Dennis Lo
Li Ka Shing Institute of Health Sciences and the Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, 3032 Ngan Shing Street, Shatin, New Territories, Hong Kong SAR, China
Nat Rev Genet 8:71-7. 2007..Since 1997, the progress of this field has been accelerated by the unexpected finding of extracellular fetal nucleic acids in maternal plasma... - SwS: a solvation web service for nucleic acidsPascal Auffinger
A R N, Universite Louis Pasteur, IBMC CNRS, Strasbourg, France
Bioinformatics 23:1035-7. 2007..This web service has been designed to allow a maximum of flexibility in terms of queries and has also been developed with didactic considerations in mind. AVAILABILITY: http://www-ibmc.u-strasbg.fr/arn/sws.html.. - Structure-editing of nucleic acids for selective targeting of RNAVaijayanti A Kumar
Division of Organic Chemistry, Synthesis, National Chemical Laboratory, Pune, 411008 India
Curr Top Med Chem 7:715-26. 2007The synthesis of backbone-modified nucleic acids has been an area of very intense research over the last two decades... - Electrochemical simulation of oxidation processes involving nucleic acids monitored with electrospray ionization-mass spectrometryFlorian Pitterl
Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
Anal Bioanal Chem 397:1203-15. 2010Oxidation is commonly involved in the alteration of nucleic acids giving rise to diverse effects including mutation, cell death, malignancy, and aging... - Molecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analoguesJoanna Panecka
Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Zwirki i Wigury 93, 02 089 Warsaw, Poland
J Phys Chem B 115:532-46. 2011.... - PrP interactions with nucleic acids and glycosaminoglycans in function and diseaseJerson L Silva
Centro Nacional de Ressonancia Magnetica Nuclear Jiri Jonas, Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, CCS, RJ 21941 590, Rio de Janeiro, Brazil
Front Biosci 15:132-50. 2010..we will explore the interaction of PrP with some of its most intriguing partners, such as sulfated glycans and nucleic acids. These molecules seem to play a dual role in prion biology and could be fundamental to explaining how prion .. - Constrained nucleic acids (CNA). Part 2. Synthesis of conformationally restricted dinucleotide units featuring noncanonical alpha/beta/gamma or delta/epsilon/zeta torsion angle combinationsIngrid Le Clézio
Laboratoire de Synthèse et Physico Chimie de Molécules d Intérêt Biologique UMR 5068, Universite Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 4, France
J Org Chem 70:1620-9. 2005Four dinucleotide building units of nucleic acids in which three out of six backbone torsion angles are included in a dioxaphosphorinane ring structure (D-CNA family) have been synthesized: two diastereoisomeric alpha,beta,gamma-D-CNA {.. - Alpha,beta-D-CNA induced rigidity within oligonucleotidesChristelle Dupouy
Laboratoire de Synthèse et Physico Chimie de Molécules d Intérêt Biologique UMR 5068 CNRS, Universite Paul Sabatier, 31062, Toulouse Cedex 9, France
Org Biomol Chem 6:2849-51. 2008.... - Diastereoselective synthesis of a conformationally restricted dinucleotide with predefined alpha and beta torsional angles for the construction of alpha,beta-constrained nucleic acids (alpha,beta-CNA)Ingrid Le Clézio
Laboratoire de Synthèse et Physico Chimie de Molécules d Intérêt Biologique UMR 5068, Universite Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 4, France
Org Lett 5:161-4. 2003..six-membered cyclic phosphotriester structure represents the smallest possible ring allowing the conformational locking of the alpha torsion angle at a significant positive value that is typical of many bulged regions of nucleic acids. - Watson-Crick base-pairing properties of nucleic acid analogues with stereocontrolled alpha and beta torsion angles (alpha,beta-D-CNAs)Christelle Dupouy
, UMR 5068 CNRS, , 31062 Toulouse Cedex 9, France
Angew Chem Int Ed Engl 45:3623-7. 2006 - [Glyoxal: a possible polyvalent substitute for formaldehyde in pathology?]Nathalie Marcon
Equipe d accueil signalisation et génomique fonctionnelle en recherche translationnelle oncologique, Service d Anatomie et Cytologie Pathologiques, Hopitaux de Brabois, CHU de Nancy, Universite de Nancy, 5, Allee du Morvan, 54511 Vandoeuvre les Nancy, France
Ann Pathol 29:460-7. 2009..advocating its substitution with less dangerous chemicals and the fact that formalin is a poor preserver of nucleic acids. Among the non-alcoholic formalin substitute, glyoxal has been hailed as the best alternative... - Crystallographic studies of chemically modified nucleic acids: a backward glanceMartin Egli
Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232 0146, USA
Chem Biodivers 7:60-89. 2010Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications... - Luminescent probes for ultrasensitive detection of nucleic acidsLev N Krasnoperov
Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, 151 Tiernan Hall, University Heights, Newark, New Jersey 07102, USA
Bioconjug Chem 21:319-27. 2010.... - Self-assembled micronanoplexes for improved biolistic delivery of nucleic acidsSergei A Svarovsky
Center for Innovations in Medicine at the Biodesign Institute, and the School of Life Sciences, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287 5901, USA
Mol Pharm 6:1927-33. 2009A new method for biolistic delivery of nucleic acids using a combination of cationic micro- and nanoparticles is reported... - Automated nucleic acids isolation using paramagnetic microparticles coupled with electrochemical detectionDalibor Huska
Department of Chemistry and Biochemistry, Mendel University of Agriculture and Forestry, Zemedelska 1, CZ 613 00 Brno, Czech Republic
Talanta 79:402-11. 2009..5h. Moreover, we applied the optimized procedure on fully automated pipetting instrument to isolate mRNA. The instrument was successfully tested on the analysis of extracts from roots of maize plants treated with cadmium(II) ions... - A research-based tumor tissue bank of gynecologic oncology: characteristics of nucleic acids extracted from normal and tumor tissues from different sitesT Y Chu
Department of Obstetrics, Tri Service General Hospital, 325, Section 2, Chengon Road, Taipei 114, Taiwan, R O C
Int J Gynecol Cancer 12:171-6. 2002..that is approaching the research requirements of modern molecular oncology and compared characteristics of nucleic acids extracted from preserved tissues... - Rapid preparation of total nucleic acids from E. coli for multi-purpose applicationsLin Cheng
Department of Biotechnology, College of Life Sciences, Wuhan University, Wuhan, Hubei 439972, China
J Biochem Mol Biol 37:351-5. 2004..We report here a simple, fast, reliable, and cost-effective method to extract total nucleic acids from E. coli by direct lysis of the cells with phenol... - Using molecular beacons for sensitive fluorescence assays of the enzymatic cleavage of nucleic acidsChaoyong James Yang
Center for Research at Bio/nano Interface, UF Genetics Institute and Shands Cancer Center, and Department of Chemistry, University of Florida, Gainsville, FL, USA
Methods Mol Biol 335:71-81. 2006..With its simplicity, convenience, high sensitivity, and excellent reproducibility, this method has the potential to be used in the study of both natural and artificial nucleic acid-cleaving enzymes... - Entamoeba histolytica: observations on metabolism based on the genome sequenceIain J Anderson
Department of Parasite Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
Exp Parasitol 110:173-7. 2005..histolytica. The usual eukaryotic glucose transporters are not present, but members of a prokaryotic monosaccharide transporter family are present... - Modeling metal cation-phosphate interactions in nucleic acids: activated dissociation of Mg+, Al+, Cu+, and Zn+ complexes of triethyl phosphateChunhai Ruan
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
J Am Chem Soc 131:10918-28. 2009..The binding of metal cations to TEP is compared to that of the nucleobases to assess the binding preferences of metal cations to nucleic acids. - A role for the MS analysis of nucleic acids in the post-genomics ageDaniele Fabris
Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA
J Am Soc Mass Spectrom 21:1-13. 2010The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years... - In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteinsEric Dausse
INSERM U386, , , France
Methods Mol Biol 288:391-410. 2005..We describe here methods successfully used in our laboratory for the selection of RNA or DNA aptamers against an RNA structure (the transactivation response element of HIV-1) and a protein (the human ribonuclease H1)... - Probing the limits of liquid droplet laser desorption mass spectrometry in the analysis of oligonucleotides and nucleic acidsJan Hoffmann
Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Str 7, 60438 Frankfurt M, Germany
Rapid Commun Mass Spectrom 23:2176-80. 2009..the advantages of LILBID mass spectrometry (laser-induced liquid bead ion desorption) in the analysis of nucleic acids and large oligonucleotides... - Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopyRobert Hänsel
Institute of Biophysical Chemistry, Goethe University, Max von Laue Str 9, 60438 Frankfurt am Main, Germany
J Am Chem Soc 131:15761-8. 2009..in different cellular environments is a well-established technique that, however, has not been applied to nucleic acids so far... - Intercalating nucleic acids: the influence of linker length and intercalator type on their duplex stabilitiesUlf B Christensen
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense, Denmark
Nucleosides Nucleotides Nucleic Acids 23:207-25. 2004Six new examples of intercalating nucleic acids were synthesized in order to evaluate the dependence of the length of the linker between oligo and intercalator on the thermal stability of their corresponding duplexes and triplexes. - A library of IR bands of nucleic acids in solutionMartina Banyay
Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, S-106 91, Stockholm, Sweden
Biophys Chem 104:477-88. 2003This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations... - Oxidative damage to nucleic acids in motor neurons containing mercuryR Pamphlett
Department of Pathology, The University of Sydney, New South Wales, Australia
J Neurol Sci 159:121-6. 1998..The findings support the hypothesis that an environmental toxin such as mercury can enter and damage motor neurons... - Oligomeric nucleic acids as antiviralsAlessandra Mescalchin
Institute of Molecular Medicine, University of Lubeck, Center for Structural and Cell Biology in Medicine CSCM, Ratzeburger Allee 160, D 23538 Lubeck, Germany
Molecules 16:1271-96. 2011Based on the natural functions and chemical characteristics of nucleic acids, a variety of novel synthetic drugs and tools to explore biological systems have become available in recent years... - The Effect of dye-dye interactions on the spatial resolution of single-molecule FRET measurements in nucleic acidsNicolas Di Fiori
Department of Physics, Boston University, Boston, Massachusetts, USA
Biophys J 98:2265-72. 2010..Second, these results are useful when deciding which dye pairs to use for nucleic acids analyses using FRET. - Interaction of antimalarial drug quinacrine with nucleic acids of variable sequence studied by spectroscopic methodsL Rivas
Instituto de Estructura de la Materia, CSIC, Serrano, Madrid, Spain
J Biomol Struct Dyn 18:371-83. 2000..The interaction of QA with the above nucleic acids lead to a different change in the chain stability and flexibility which is further related to the different .. - Improved method for simultaneous isolation of proteins and nucleic acidsSoroth Chey
Institute of Virology, University of Leipzig, Leipzig, Germany
Anal Biochem 411:164-6. 2011..This technique allows a fast (30min) and efficient (with a protein recovery of up to 95%) extraction of proteins for the study of transcriptional and posttranscriptional events from the same sample... - Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?Jiri Sponer
Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
J Phys Chem B 114:15723-41. 2010..a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics... - Modeling metal cation-phosphate interactions in nucleic acids in the gas phase via alkali metal cation-triethyl phosphate complexesChunhai Ruan
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
J Phys Chem A 111:13521-7. 2007..The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate... - Frontiers of mass spectrometry in nucleic acids analysisHerbert Oberacher
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
Eur J Mass Spectrom (Chichester, Eng) 16:351-65. 2010b>Nucleic acids research is a highly competitive field of research. A number of well established methods are available... - PubDNA Finder: a web database linking full-text articles to sequences of nucleic acidsMiguel Garcia-Remesal
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... - 1H-1H correlations across N-H...N hydrogen bonds in nucleic acidsA Majumdar
Cellular Biochemistry and Biophysics Department, Memorial Sloan Kettering Cancer Center, New York 10021, USA
J Biomol NMR 21:289-306. 2001..pulse sequences to obtain direct, internucleotide correlations between protons in uniformly 13C/15N labeled nucleic acids containing Nd...HNa hydrogen bonds... - Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structuresPradeep S Pallan
Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
Nat Protoc 2:647-51. 2007..The estimated time for the synthesis and HPLC purification of oligonucleotides with incorporated 2'-SeMe-uridine residues is approximately 46 h for 'trityl on' and approximately 32 h for 'trityl off' methods, respectively... - Detection of circulating fetal nucleic acids: a review of methods and applicationsE C W Hung
Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and Department of Chemical Pathology, The Chinese University of Hong Kong, China
J Clin Pathol 62:308-13. 2009The discovery of cell-free circulating fetal nucleic acids in maternal plasma has opened up new possibilities in non-invasive prenatal diagnosis... - Mixed chelate copper complex, Casiopeina IIgly, binds and degrades nucleic acids: a mechanism of cytotoxicityAdolfo Rivero-Muller
School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 5XH, UK
Chem Biol Interact 165:189-99. 2007..The generation of 8-oxodG in cells exposed to casIIgly suggests that the generation of ROS is the major cause of the cytotoxicity observed and underlies the high toxicity and anticancer activity of these compounds... - Circulating nucleic acids in cancer and pregnancyPamela Pinzani
Department of Clinical Physiopathology, University of Florence and Istituto Toscano Tumori, Viale Pieraccini 6, 50139 Florence, Italy
Methods 50:302-7. 2010Circulating nucleic acids are present in the blood of humans and other vertebrates... - Force field parameters for rotation around chi torsion axis in nucleic acidsHirotaka Ode
Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263 8522, Japan
J Comput Chem 29:2531-42. 2008To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis... - Cations as mediators of the adsorption of nucleic acids on clay surfaces in prebiotic environmentsMarco Franchi
Department of Animal Biology and Genetics, University of Florence, Italy
Orig Life Evol Biosph 33:1-16. 2003..Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay... - Inhibition of pre-mRNA splicing by synthetic branched nucleic acidsSandra Carriero
Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke St West, Montreal, QC, H3A 2K6, Canada
Nucleic Acids Res 31:6157-67. 2003..The data obtained suggest that binding and sequestering of a branch recognition factor by the branched nucleic acids is an early event, which occurs prior to the first chemical step of splicing... - Triplex formation by pyrene-labelled probes for nucleic acid detection in fluorescence assaysIneke Van Daele
Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
Chembiochem 9:791-801. 2008..5 degrees C and a Phi(F) of 0.158 at pH 6.0. Under similar conditions, a Watson-Crick-type duplex formed with the latter probe showed lower fluorescence intensity (Phi(F)=0.081) than for the triplex... - Enzymatic resolution and base pairing properties of D- and L-cyclohexenyl nucleic acids (CeNA)Ping Gu
Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
Nucleosides Nucleotides Nucleic Acids 24:993-8. 2005..CeNAs of opposite chirality form a self-pairing system on their own... - Presence of 2',5'-linkages in a homopyrimidine DNA oligonucleotide promotes stable triplex formation under physiological conditionsSatoshi Obika
Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
Nucleosides Nucleotides Nucleic Acids 24:1055-8. 2005.... - Probing nucleic acid structure with shape-selective rhodium and ruthenium complexesB A Jackson
California Institute of Technology, Pasadena, California, USA
Curr Protoc Nucleic Acid Chem . 2001..Complex formation is easily detected by light-induced nucleic acid cleavage. The modular construction of the complexes makes it possible to generate probes to examine a wide variety of structural characteristics of nucleic acids. - Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble basesJan C Biro
Homulus Foundation, 612 S Flower Str, 1220, Los Angeles, CA 90017, USA
Theor Biol Med Model 5:14. 2008..The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences... - Synthesis and properties of a novel bridged nucleic acid analogue, 5'-amino-3',5'-BNAMitsuaki Sekiguchi
Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
Nucleosides Nucleotides Nucleic Acids 24:1097-100. 2005..The melting temperature (Tm) of the duplex comprising the 5'-amino-3',5'-BNA and its complementary strand was much higher than that of the duplex containing the corresponding 5-amino-DNA... - Data mining of molecular dynamics trajectories of nucleic acidsAgnes Noy
Institut de Recerca Biomedica Barcelona, Parc Cientific de Barcelona, Josep Samitier 1 5, Barcelona E 08028 Spain
J Biomol Struct Dyn 23:447-56. 2006..In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids. - Synthesis of two mirror image 4-helix junctions derived from glycerol nucleic acidRichard S Zhang
Center for BioOptical Nanotechnology, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287 1604, USA
J Am Chem Soc 130:5846-7. 2008..We synthesized two 4-helix junctions based entirely on GNA self-pairing and showed that GNA provides easy access to highly stable nanostructures with left- and right-handed helical configurations... - Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation studyAndre Barthel
School of Engineering and Science, International University Bremen, D 28759 Bremen, Germany
Biophys J 90:2450-62. 2006.... - Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid basesXiang Li
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
J Chem Phys 127:174309. 2007..The new valence states observed here, unlike dipole bound states, could exist in condensed phases and may be relevant to radiobiological damage... - Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotidesMartin Egli
Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
Annu Rev Biophys Biomol Struct 36:281-305. 2007Chemically modified nucleic acids function as model systems for native DNA and RNA; as chemical probes in diagnostics or the analysis of protein-nucleic acid interactions and in high-throughput genomics and drug target validation; as .. - Kinetics of protein-release by an aptamer-based DNA nanodeviceA Reuter
Department of Physics and Center for Nanoscience, LMU Munchen, Geschwister Scholl Platz 1, 80539, Munich, Germany
Eur Phys J E Soft Matter 22:33-40. 2007..The results from the experiments and a numerical simulation support the view that the DNA effector strand first binds to the aptamer device followed by the displacement of the protein... - Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistryRoberto Corradini
Dipartimento di Chimica Organica e Industriale, Universita di Parma, I 4310 Parma, Italy
Chirality 19:269-94. 2007..with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA .. - Mixed-sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding propertiesRoberta J Worthington
School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, UKM1 7DN
Org Biomol Chem 5:249-59. 2007.... - Helical structures from an isotropic homopolymer modelJames E Magee
School of Chemical Engineering and Analytical Science, The University of Manchester, P O Box 88, Sackville Street, Manchester M60 1QD, United Kingdom
Phys Rev Lett 96:207802. 2006..We investigate how this behavior depends upon the ratio between bond length and monomer radius...
Research Grants
- Invader LNAs as Novel Gene Specific TherapeuticsMADHUSUDHAN REDDY PAPASANI; Fiscal Year: 2010..area has been achieved with triplex forming oligonucleotides, minor groove binding polyamides, and peptide nucleic acids, but major methodological limitations have impeded development of drug candidates...
- DEVELOPING SOLUTES AS STRUCTURAL/MECHANISTIC PROBES OF PROTEIN-DNA INTERACTIONSM Thomas Record; Fiscal Year: 2011..to as solutes) exert often large, specific effects on fundamental biological processes involving proteins and nucleic acids (e.g. folding, assembly, binding, aggregation)...
- DEVELOPING SOLUTES AS STRUCTURAL/MECHANISTIC PROBES OF PROTEIN-DNA INTERACTIONSM Thomas Record; Fiscal Year: 2010..to as solutes) exert often large, specific effects on fundamental biological processes involving proteins and nucleic acids (e.g. folding, assembly, binding, aggregation)...
- Cell-targeting peptide nucleic acids for hormone-refractory prostate cancerBeverly Barton; Fiscal Year: 2007..New treatments are urgently needed. Malignant cells become dependent upon STAT3 for survival. Peptide nucleic acids (PNAs) are DNA mimics, wherein the phosphodiester backbones are replaced by neutrally-charged polyamines...
- ELECTRO-OPTIC TECHNIQUES IN ELECTROPHORESISMichael Morris; Fiscal Year: 1993..in electrophoresis gels and apply these results to novel forms of gel electrophoresis and detection of nucleic acids and proteins in gels. Both slab gel and capillary formats will be investigated...
- Computational Suite for RNA-Targeted Drug DesignErin Duffy; Fiscal Year: 2005..Importantly, the antibiotics principally and nearly exclusively interact with the nucleic acids and ions in the SOS ribosomal subunit; that is, protein ligand interactions are largely absent in these ..
- STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDSPETER HANS VON HIPPEL; Fiscal Year: 2010..Such targets can then be exploited to develop specific tools and reagents to control diseases of anomalous cellular development, including various forms of cancer and other genetic diseases. ..
- Illuminating the Mechanistic Pathways of Polymer-Mediated Nucleic Acid DeliveryTHERESA REINEKE; Fiscal Year: 2009..The intracellular delivery of nucleic acids to study these processes offers unprecedented promise for revolutionizing biomedical research and drug ..
- Invader LNAs as Novel Gene Specific TherapeuticsPATRICK HRDLICKA; Fiscal Year: 2009..area has been achieved with triplex forming oligonucleotides, minor groove binding polyamides, and peptide nucleic acids, but major methodological limitations have impeded development of drug candidates...
- Investigation of the role of bacteria in the sarcoidosis trimolecular complexWonder Drake; Fiscal Year: 2007..and IS6110 in 25 sarcoidosis and 25 control paraffin- embedded specimens and noted evidence of mycobacterial nucleic acids in 60% of the sarcoid granulomas and none of the controls (p<0.00002, chi square)...
- MODIFIED NUCLEOSIDE STRUCTURE FUNCTION RELATIONS--TRNAPAUL AGRIS; Fiscal Year: 1993Modified nucleosides impart unique site-specific properties to nucleic acids, yet determining their significance to structure-function relationships has proven difficult...
- Microchip to Detect Influenza Infection and Type in Nasopharyngeal SwabsCatherine Klapperich; Fiscal Year: 2009..These devices are capable of lysing viral particles and binding, concentrating and eluting nucleic acids from influenza infected mammalian samples of 10 l or less...