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Journal Articles: 34 results
A-DNA and B-DNA: Comparing Their Historical X-ray Fiber Diffraction Images  Amand A. Lucas
This paper provides a comparative explanation of the structural content of the diffraction diagrams of A-DNA and B-DNA that facilitated the discovery of the double-helical structure of DNA by Watson and Crick in 1953. This analysis is supported a method that simulates both A-DNA and B-DNA X-ray images optically.
Lucas, Amand A. J. Chem. Educ. 2008, 85, 737.
Biophysical Chemistry |
Conformational Analysis |
Crystals / Crystallography |
X-ray Crystallography |
Nucleic Acids / DNA / RNA
Observation of DNA Molecules Using Fluorescence Microscopy and Atomic Force Microscopy  Takashi Ito
Describes procedures for an instrumental analysis laboratory to observe individual double-stranded DNA (dsDNA) molecules using fluorescence and atomic force microscopy; immobilization of dsDNA molecules on a planar substrate in their stretched form permits students to measure the size of the dsDNA molecules using these microscopic techniques.
Ito, Takashi. J. Chem. Educ. 2008, 85, 680.
Biophysical Chemistry |
Biotechnology |
Fluorescence Spectroscopy |
Nanotechnology |
Surface Science |
Nucleic Acids / DNA / RNA
Fluorescence Spectroscopy of tRNAPhe Y Base in the Presence of Mg2+ and Small Molecule Ligands  Sarah R. Kirk, Todd P. Silverstein, and Karen L. McFarlane Holman
This article describes a set of experiments in which ligands (e.g., spermine, neomycin B, magnesium) are titrated into tRNAPhe solution and fluorescence spectroscopy is used to draw conclusions on how different binding modes affect tRNAPhe tertiary structure.
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane. J. Chem. Educ. 2008, 85, 678.
Bioinorganic Chemistry |
Bioorganic Chemistry |
Biophysical Chemistry |
Fluorescence Spectroscopy |
Nucleic Acids / DNA / RNA
Metal-Catalyzed Cleavage of tRNAPhe  Sarah R. Kirk, Todd P. Silverstein, and Karen L. McFarlane Holman
This article describes a set of experiments in which students study tRNAPhe conformational changes induced by ligand binding using gel electrophoresis to determine how metal-catalyzed hydrolysis is affected by parameters such as tRNAPhe structure, ligand charge, and the chemistry of the metal ion complexes involved.
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane. J. Chem. Educ. 2008, 85, 676.
Bioinorganic Chemistry |
Bioorganic Chemistry |
Electrophoresis |
Nucleic Acids / DNA / RNA
UV Thermal Melting Curves of tRNAPhe in the Presence of Ligands  Sarah R. Kirk, Todd P. Silverstein, and Karen L. McFarlane Holman
This article describes a set of experiments in which the thermal unfolding of tRNAPhe is studied with UVvis spectrophotometry. Students examine the effects of magnesium and small molecule ligands on tRNAPhe conformational stability and draw conclusions about tRNAPhe ligand binding modes and the impact of various types of ligands on tRNA structure.
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane. J. Chem. Educ. 2008, 85, 674.
Bioinorganic Chemistry |
Bioorganic Chemistry |
Biophysical Chemistry |
Thermal Analysis |
UV-Vis Spectroscopy |
Nucleic Acids / DNA / RNA
Probing Changes in the Conformation of tRNAPhe: An Integrated Biochemistry Laboratory Course  Sarah R. Kirk, Todd P. Silverstein, Karen L. McFarlane Holman, and Buck L. H. Taylor
This guided-inquiry, laboratory course focuses on the biomolecule tRNAPhe and combines biochemistry with elements of bioorganic and bioinorganic chemistry. Throughout the semester students work collaboratively to study tRNAPhe structure and the influence of ligand binding under a variety of conditions using several analytical techniques.
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane; Taylor, Buck L. H. J. Chem. Educ. 2008, 85, 666.
Bioinorganic Chemistry |
Bioorganic Chemistry |
Biophysical Chemistry |
Electrophoresis |
Fluorescence Spectroscopy |
UV-Vis Spectroscopy |
Student-Centered Learning |
Nucleic Acids / DNA / RNA
Molecular Models of DAPI  William F. Coleman
This months Featured Molecule is DAPI (4',6-diamidino-2-phenylindole), a minor-groove binder to DNA.
Coleman, William F. J. Chem. Educ. 2007, 84, 1307.
Proteins / Peptides |
Nucleic Acids / DNA / RNA
Quantitative Determination of DNA–Ligand Binding Using Fluorescence Spectroscopy  Eamonn F. Healy
The experiment described here measures the DAPI (4',6-diamidino-2-phenylindole) binding constant for calf-thymus DNA using fluorescence measurements and a modified Scatchard analysis. Student can estimate DAPI occupancy of the minor groove in DNA by calculating the number of nucleotides per bound ligand.
Healy, Eamonn F. J. Chem. Educ. 2007, 84, 1304.
Bioanalytical Chemistry |
Drugs / Pharmaceuticals |
Fluorescence Spectroscopy |
Medicinal Chemistry |
Nucleic Acids / DNA / RNA
X-ray Diffraction and the Discovery of the Structure of DNA  David T. Crouse
Describes a step-by-step method of teaching the X-ray diffraction analysis of DNA using the approach employed by Watson, Crick, Wilkins, Franklin, and Gosling. Excerpts of their original articles describe the obstacles encountered by these researchers, the contributions made by each, and the degree to which X-ray diffraction aided their determination of DNA's structure.
Crouse, David T. J. Chem. Educ. 2007, 84, 803.
Biophysical Chemistry |
Crystals / Crystallography |
X-ray Crystallography |
Molecular Properties / Structure |
Molecular Modeling |
Nucleic Acids / DNA / RNA
Using Physical Models of Biomolecular Structures To Teach Concepts of Biochemical Structure and Structure Depiction in the Introductory Chemistry Laboratory  Gordon A. Bain, John Yi, Mithra Beikmohamadi, Timothy M. Herman, and Michael A. Patrick
Custom-made physical models of alpha-helices and beta-sheets, the zinc finger moiety, beta-globin, and green fluorescent protein are used to introduce students in first-year chemistry to the primary, secondary, and tertiary structure of proteins.
Bain, Gordon A.; Yi, John; Beikmohamadi, Mithra; Herman, Timothy M.; Patrick, Michael A. J. Chem. Educ. 2006, 83, 1322.
Amino Acids |
Proteins / Peptides |
Molecular Modeling |
Molecular Properties / Structure |
Nucleic Acids / DNA / RNA
A Unique Demonstration Model of DNA  Jonathan P. L. Cox
Describes a physical demonstration model of DNA for the classroom. The model comprises two types of building blocks that can be put together rapidly to produce an abstract structure that portrays several of the gross architectural features of idealized B-DNA.
Cox, Jonathan P. L. J. Chem. Educ. 2006, 83, 1319.
Molecular Biology |
Molecular Properties / Structure |
Student-Centered Learning |
Nucleic Acids / DNA / RNA
Label-Free Detection of DNA Hybridization by Cyclic Voltammetry. An Advanced Undergraduate Analytical Chemistry Laboratory Experiment  Temitope Aiyejorun, Janusz Kowalik, Jiri Janata, and Mira Josowicz
Describes a set of experiments designed to explore several concepts relevant to electropolymerization of intrinsically conducting polymers, their use as an electrically controlled ion-exchanger of chloride ions, and their ability to bind oligonucleotides through a noncovalent interaction with magnesium ions used as a linker between the polymer and the DNA strand.
Aiyejorun, Temitope; Kowalik, Janusz; Janata, Jiri; Josowicz, Mira. J. Chem. Educ. 2006, 83, 1208.
Biophysical Chemistry |
Electrochemistry |
Kinetics |
Undergraduate Research |
Nucleic Acids / DNA / RNA
DNA Profiling of the D1S80 Locus: A Forensic Analysis for the Undergraduate Biochemistry Laboratory  D. Dewaine Jackson, Chad S. Abbey, and Dylan Nugent
Describes a laboratory exercise in DNA profiling that can be used to demonstrate four fundamental procedures: isolation of genomic DNA from human cells, use of the polymerase chain reaction to amplify DNA, separation of amplified DNAs on agarose and polyacrylamide gels, and quantitative analysis of data (while comparing two different gel separation techniques).
Jackson, D. Dewaine; Abbey, Chad S.; Nugent, Dylan. J. Chem. Educ. 2006, 83, 774.
Biological Cells |
Biotechnology |
Electrophoresis |
Forensic Chemistry |
Molecular Biology |
Quantitative Analysis |
Nucleic Acids / DNA / RNA
Cytochrome c: A Biochemistry Laboratory Course  John B. Vincent and Stephen A. Woski
A unified biochemistry laboratory course has been developed. Rather than using miscellaneous laboratory experiments, the concept behind this course is to focus on a theme: the process of biochemical research. The laboratory deals entirely with one protein, cytochrome c, simulating the experience of a real-world research project. The laboratory is built around team-learning: groups of students isolate cytochrome c, characterize it by a variety of biochemical and bioinorganic methods, attempt to determine its function, and finally alter the protein to produce a modifier of oxidative nucleic acid damage.
Vincent, John B.; Woski, Stephen A. J. Chem. Educ. 2005, 82, 1211.
Bioinorganic Chemistry |
Proteins / Peptides |
Chromatography |
Electrophoresis |
Enzymes |
EPR / ESR Spectroscopy |
NMR Spectroscopy |
Nucleic Acids / DNA / RNA |
UV-Vis Spectroscopy
Testing for Ultraviolet Toxicity Using Fungi  Marcelo Vital and Patricia Esperón
In this article, we describe a laboratory project quantifying the effects of UV radiation on a suspension of living cells. This laboratory experiment was designed for undergraduate students in biochemistry. The experiment was carried out employing different fungi strains, changing the dosage of radiation, the distance to the UV source, and the exposure period to the UV radiation. The quantity of viable spores was calculated and the doseresponse curves were drawn. Students were able to prove that 100% of mortality was achieved with the longest time of exposure.
Vital, Marcelo; Esperón, Patricia. J. Chem. Educ. 2005, 82, 926.
Nucleic Acids / DNA / RNA |
UV-Vis Spectroscopy |
Medicinal Chemistry |
Molecular Biology |
Photochemistry
Testing for Genetically Modified Foods Using PCR  Ann Taylor and Samin Sajan
The polymerase chain reaction (PCR) is a powerful technique used to detect and amplify a specific DNA sequence. In this experiment, DNA is isolated from commercially available corn meal and corn-muffin mixes, then a sequence unique to transgenic plants is amplified by PCR. The amplified sequence is identified by its size (192 base pairs) by agarose gel electrophoresis. This experiment could be used in either a biochemistry course or in an analytical chemistry course in a curriculum that integrates biochemistry throughout the course work.
Taylor, Ann; Sajan, Samin. J. Chem. Educ. 2005, 82, 597.
Agricultural Chemistry |
Constitutional Isomers |
Biotechnology |
Plant Chemistry |
Consumer Chemistry |
Nucleic Acids / DNA / RNA
A 3D Model of Double-Helical DNA Showing Variable Chemical Details  Susan G. Cady
A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance the basic helical frame to show the shapes and sizes of the nitrogenous base rings, 3' and 5' chain termini, and base pair hydrogen bonding. Students can incorporate random or real gene sequence data into their models.
Cady, Susan G. J. Chem. Educ. 2005, 82, 79.
Biotechnology |
Molecular Properties / Structure |
Molecular Modeling |
Nucleic Acids / DNA / RNA
Does Active Learning through an Antisense Jigsaw Make Sense?  Mahadevan Seetharaman and Karin Musier-Forsyth
Three journal articles on nucleic acid antisense modification strategies were assigned to 12 students as part of an active learning "jigsaw" exercise for a graduate-level chemistry course on nucleic acids. The effectiveness of this active learning strategy and its applicability to other topics are discussed in this article.
Seetharaman, Mahadevan; Musier-Forsyth, Karin. J. Chem. Educ. 2003, 80, 1404.
Learning Theories |
Nucleic Acids / DNA / RNA
Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment  Vladimir Shafirovich, Carolyn Singh, and Nicholas E. Geacintov
This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNAagarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage.
Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E. J. Chem. Educ. 2003, 80, 1297.
Biophysical Chemistry |
Drugs / Pharmaceuticals |
Photochemistry |
Aromatic Compounds |
Nucleic Acids / DNA / RNA
Analysis of DAPI and SYBR Green I as Alternatives to Ethidium Bromide for Nucleic Acid Staining in Agarose Gel Electrophoresis  Kevin M. Bourzac, Lori J. LaVine, and Margaret S. Rice
DAPI and SYBR Green I are good staining alternatives to ethidium bromide in that they have similar sensitivity and are both easy to use. SYBR Green I is more expensive than EB or DAPI; however, the limited safety data suggest that SYBR Green I is the safest stain.
Bourzac, Kevin M.; LaVine, Lori J.; Rice, Margaret S. J. Chem. Educ. 2003, 80, 1292.
Dyes / Pigments |
Electrophoresis |
Nucleic Acids / DNA / RNA
Allele-Specific Polymerase Chain Reaction-Based Genotyping of a Normal Variation in Human Color Vision  Beth Wilson, Ira M. Lubin, and Kathryn B. Grant
Students utilize microcentrifugation and silica-gel column chromatography to extract DNA from their own buccal (cheek) epithelial cells. The polymerase chain reaction and agarose gel electrophoresis are then employed to identify a single nucleotide polymorphism that is responsible for a commonly encountered variation in human red color vision.
Wilson, Beth; Lubin, Ira M.; Grant, Kathryn B. J. Chem. Educ. 2003, 80, 1289.
Biotechnology |
Electrophoresis |
Nucleic Acids / DNA / RNA
Identification of Forensic Samples via Mitochondrial DNA in the Undergraduate Biochemistry Laboratory  Julie T. Millard and André M. Pilon
Identification of forensic samples via mitochondrial DNA in a hypothetical kidnapping case.
Millard, Julie T.; Pilon, André M. J. Chem. Educ. 2003, 80, 444.
Quantitative Analysis |
Electrophoresis |
Separation Science |
Biotechnology |
Forensic Chemistry |
Applications of Chemistry |
Nucleic Acids / DNA / RNA
Genetic Code Wordsearch  Terry L. Helser
Wordsearch puzzle containing 30 words that describe the nucleotide sequences used to produce proteins.
Helser, Terry L. J. Chem. Educ. 2003, 80, 417.
Biotechnology |
Nomenclature / Units / Symbols |
Enrichment / Review Materials |
Nucleic Acids / DNA / RNA
Visualizing Atoms, Molecules, and Surfaces by Scanning Probe Microscopy  Kimberly Aumann, Karen J. C. Muyskens, and Kumar Sinniah
Examples of applications of scanning probe microscopy (SPM) in an undergraduate curriculum; includes investigating DNA, analysis of microchip memory arrays and circuitry, and visualizing filamentous actin.
Aumann, Kimberly; Muyskens, Karen J. C.; Sinniah, Kumar. J. Chem. Educ. 2003, 80, 187.
Atomic Properties / Structure |
Instrumental Methods |
Materials Science |
Nanotechnology |
Surface Science |
Undergraduate Research |
Nucleic Acids / DNA / RNA
Experimental Design and Polyelectrolyte Effects on Ligand Binding to Nucleic Acids. An Undergraduate Biochemistry Lab  Matthew A. Fisher, Danielle Johnston, and Daniel A. Ritt
Investigation involving the binding of the polyamine spermine to DNA as a function of cations in solution.
Fisher, Matthew A.; Johnston, Danielle; Ritt, Daniel A. J. Chem. Educ. 2002, 79, 374.
Biophysical Chemistry |
Amines / Ammonium Compounds |
Nucleic Acids / DNA / RNA
Nucleic Acids: Structures, Properties, and Functions (by Victor A. Bloomfield, Donald M. Crothers, and Ignacio Tinoco Jr.; with contributions from John E. Hearst, David E. Wemmer, Peter A. Kollman, and Douglas H. Turner)  John H. Shibata
A single volume that contains a comprehensive and detailed account of the structures and physical properties of nucleic acids.
Shibata, John H. J. Chem. Educ. 2001, 78, 314.
Molecular Biology |
Molecular Properties / Structure |
Nucleic Acids / DNA / RNA
DNA Topology Analysis in the Undergraduate Biochemistry Laboratory  Michael V. Keck
A set of complementary experiments is described which are useful in teaching the principles of DNA topology to undergraduate biochemistry students.
Keck, Michael V. J. Chem. Educ. 2000, 77, 1471.
Drugs / Pharmaceuticals |
Electrophoresis |
Molecular Properties / Structure |
Nucleic Acids / DNA / RNA
Thermodynamics of DNA Duplex Formation: A Biophysical Chemistry Laboratory Experiment  Kathleen P. Howard
The goal of this biophysical experiment is to measure thermodynamic properties of a short DNA duplex by melting the ordered native structure (duplex) into the disordered, denatured state (single strands) while monitoring the transition using ultraviolet spectrophotometry.
Howard, Kathleen P. J. Chem. Educ. 2000, 77, 1469.
Biophysical Chemistry |
Thermodynamics |
UV-Vis Spectroscopy |
Nucleic Acids / DNA / RNA
Genomics: The Science and Technology Behind the Human Genome Project (by Charles R. Cantor and Cassandra L. Smith)  reviewed by Martin J. Serra
This book is an outgrowth of a series of lectures given by one of the former heads (CRC) of the Human Genome Initiative. The book is designed to reach a wide audience, from biologists with little chemical or physical science background through engineers, computer scientists, and physicists with little current exposure to the chemical or biological principles of genetics.
Serra, Martin J. J. Chem. Educ. 2000, 77, 33.
Biotechnology |
Nucleic Acids / DNA / RNA
Liver and Onions: DNA Extraction from Animal and Plant Tissues  Karen J. Nordell, Anne-Marie L. Jackelen, S. Michael Condren, George C. Lisensky, and Arthur B. Ellis*
This activity, which allows students to extract DNA from plant and animal cells, serves as a spectacular example of the complexity of biochemical structure and function and fits well with a discussion of nucleic acids, hydrogen bonding, genetic coding, and heredity. DNA extraction can also be used in conjunction with a discussion of polymers and their properties.
Nordell, Karen J.; Jackelen, Anne-Marie L.; Condren, S. Michael; Lisensky, George C.; Ellis, Arthur B. J. Chem. Educ. 1999, 76, 400A.
Hydrogen Bonding |
Molecular Properties / Structure |
Nucleic Acids / DNA / RNA
Chromatin Isolation and DNA Sequence Analysis in Large Undergraduate Laboratory Sections  Ann E. Hagerman
One exercise is a simple laboratory experiment in which chromatin is isolated from chicken liver and is resolved into histone proteins and DNA by ion-exchange chromatography. The other is a series of computer simulations that introduce DNA sequencing, mapping, and sequence analysis to the students.
Hagerman, Ann E. J. Chem. Educ. 1999, 76, 1426.
Biotechnology |
Proteins / Peptides |
Nucleic Acids / DNA / RNA
Monitoring Hammerhead Ribozyme-Catalyzed Cleavage with a Fluorescein-Labeled Substrate: Effects of Magnesium Ions and Antibiotic Inhibitors. A Biochemistry Laboratory: Part 2  Christine S. Chow, Smita Somne, and Beatriz Llano-Sotelo
An experiment is presented that demonstrates current techniques in modern RNA research and introduces a method for nonradioactive monitoring of RNA reactions. The laboratory involves the study of hammerhead ribozyme activity and the influence of metal ions and antibiotics on these important RNA-based reactions.
Chow, Christine S.; Somne, Smita; Sotelo, Beatriz Llano. J. Chem. Educ. 1999, 76, 651.
Bioorganic Chemistry |
Electrophoresis |
Enzymes |
Bioinorganic Chemistry |
Nucleic Acids / DNA / RNA
Synthesis and Purification of a Hammerhead Ribozyme and a Fluorescein-Labeled RNA Substrate. A Biochemistry Laboratory: Part 1  Christine S. Chow and Smita Somne
The applications of in vitro transcription and chemical synthesis of RNA are discussed. This laboratory describes the in vitro synthesis of a 38-nucleotide hammerhead ribozyme and the synthesis of a 17-nucleotide fluorescein-labeled RNA substrate by using standard phosphoramidite methodologies, two widely used methods in modern RNA research.
Chow, Christine S.; Somne, Smita. J. Chem. Educ. 1999, 76, 648.
Bioorganic Chemistry |
Electrophoresis |
Enzymes |
Bioinorganic Chemistry |
Nucleic Acids / DNA / RNA
Revealing the Backbone Structure of B-DNA from Laser Optical Simulations of Its X-ray Diffraction Diagram  A. A. Lucas, Ph. Lambin, R. Mairesse, and M. Mathot
A visible laser and a set of nine specially designed diffraction gratings held on a single slide have been used to build up progressively a classroom optical simulation of the diffraction of X-rays by a B-DNA fiber. The nine optical transforms allow understanding, without recourse to helical diffraction theory, of how the prominent features of the observed diffraction pattern arise from each of the structural parameters of the DNA backbone.
Lucas, A. A.; Lambin, Ph.; Mairesse, R.; Mathot, M. J. Chem. Educ. 1999, 76, 378.
Crystals / Crystallography |
X-ray Crystallography |
Molecular Properties / Structure |
Nucleic Acids / DNA / RNA