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'''Molecular models of DNA structures''' are representations of the molecular geometry and DNA topology|topology of Deoxyribonucleic acid (DNA) molecules using one of several means such as: closely packed spheres (CPK models) made of plastic metal wires for 'skeletal models' graphic computations and animations by computers artistic rendering and so on, with the aim of simplifying and presenting the essential physical and chemical properties of DNA molecular structures either ''in vivo'' or ''in vitro'' Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo Thus an old standing dynamic problem is how DNA "self-replication" takes place in living cells that should involve transient uncoiling of supercoiled DNA fibers Although DNA consists of relatively rigid very large elongated biopolymer molecules called "fibers" or chains (that are made of repeating nucleotide units of four basic types attached to deoxyribose and phosphate groups) its molecular structure in vivo undergoes dynamic configuration changes that involve dynamically attached water molecules and ions Supercoiling packing with histones in chromosome structures and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists Like other large molecules and biopolymers DNA often exists in multiple stable geometries (that is, it exhibits conformational isomerism) and configurational quantum states which are close to each other in energy on the potential energy surface of the DNA molecule Such geometries can also be computed at least in principle by employing ab initio quantum chemistry methods that have high accuracy for small molecules Such quantum geometries define an important class of ab initio molecular models of DNA whose exploration has barely started
In an interesting twist of roles the DNA molecule itself was proposed to be utilized for quantum computing Both DNA nanostructures as well as DNA 'computing' biochips have been built (see biochip image at right)
The more advanced computer-based molecular models of DNA involve molecular dynamics simulations as well as quantum mechanical computations of vibro-rotations delocalized molecular orbitals (MOs) electric moment]s hydrogen-bonding and so on

Importance

From the very early stages of structural studies of DNA by X-ray diffraction and biochemical means molecular models such as the Watson-Crick double-helix model were successfully employed to solve the 'puzzle' of DNA structure and also find how the latter relates to its key functions in living cells The first high quality X-ray diffraction patternsof A-DNA were reported by Rosalind Franklin and Raymond Gosling in 1953Franklin RE and Gosling RG recd6 March 1953 Acta Cryst (1953) 6, 673 The Structure of Sodium Thymonucleate Fibres I. The Influence of Water Content Acta Cryst (1953) and 6, 678 The Structure of Sodium Thymonucleate Fibres II. The Cylindrically Symmetrical Patterson Function The first calculations of the Fourier transform of an atomic helix were reported one year earlier by Cochran Crick and Vand Cochran W., Crick FHC and Vand V. 1952 The Structure of Synthetic Polypeptides 1. The Transform of Atoms on a Helix Acta Cryst 5(5):581-586 and were followed in 1953 by the computation of the Fourier transform of a coiled-coil by CrickCrick FHC 1953a The Fourier Transform of a Coiled-Coil Acta Crystallographica 6(8-9):685-689The first reports of a double-helix molecular model of B-DNA structure were made by Watson and Crick in 1953Watson JD; Crick FHC 1953a Molecular Structure of Nucleic Acids- A Structure for Deoxyribose Nucleic Acid Nature 171(4356):737-738 Watson JD; Crick FHC 1953b The Structure of DNA Cold Spring Harbor Symposia on Qunatitative Biology 18:123-131 Last-but-not-least Maurice F. WilkinsA Stokes and HR Wilson reported the first X-ray patternsof in vivo B-DNA in partially oriented salmon sperm heads The development of the first correct double-helix molecular model of DNA by Crick and Watson may not have been possible without the biochemical evidence for the nucleotide base-pairing ([1]; [2]) or Chargaff's rules
Double Helix
Discovery
William Astbury
Oswald Avery
Francis Crick
Erwin Chargaff
Max Delbrück
Jerry Donohue
Rosalind Franklin
Raymond Gosling
Phoebus Levene
Linus Pauling
Sir John Randall
Erwin Schrödinger
Alex Stokes
James Watson
Maurice Wilkins
Herbert Wilson


Examples of DNA molecular models

Animated molecular models allow one to visually explore the three-dimensional (3D) structure of DNA The first DNA model is a space-filling or CPK model of the DNA double-helix whereas the third is an animated wire or skeletal type molecular model of DNA The last two DNA molecular models in this series depict quadruplex DNA that may be involved in certain cancershttp://wwwphycamacuk/research/bss/molbiophysicsphphttp://planetphysicsorg/encyclopedia/TheoreticalBiophysicshtml The last figure on this panel is a molecular model of hydrogen bonds between water molecules in ice that are similar to those found in DNAFile:MethanolpdbpngFile:DNA-fragment-3D-vdWpngFile:BdnagifFile:Simple harmonic oscillatorgifFile:DNA chemical structuresvgFile:ADN animationgifFile:ABDNAxrgpjjpghttp://commonswikimediaorg/wiki/File:ABDNAxrgpjjpgFile:Parallel telomere quadruplepngFile:Four-way DNA junctiongifFile:DNA_replication_ensvgFile:ABDNAxrgpjjpgFile:Plos VHLjpgFile:3D model hydrogen bonds in waterjpg and B-DNA X-ray Patterns http://commonswikimediaorg/wiki/Category:DNAFile:
  • Spacefilling model or CPK model - a molecule is represented by overlapping spheres representing the atoms

Images for DNA Structure Determination from X-Ray Patterns

The following images illustrate both the principles and the main steps involved in generating structural information from X-ray diffraction studies of oriented DNA fibers with the help of molecular models of DNA that are combined with crystallographic and mathematical analysis of the X-ray patterns From left to right the gallery of images shows:
    • First row:
  • 1 Constructive X-ray interference or diffraction following Bragg's Law of X-ray "reflection by the crystal planes";
  • 2 A comparison of A-DNA (crystalline) and highly hydrated B-DNA (paracrystalline) X-ray diffraction and respectively X-ray scattering patterns (courtesy of Dr. Herbert R. Wilson FRS- see refs list);
  • 3 Purified DNA precipitated in a water jug;
  • 4 The major steps involved in DNA structure determination by X-ray crystallography showing the important role played by molecular models of DNA structure in this iterative structure--determination process;
    • Second row:
  • 5 Photo of a modern X-ray diffractometer employed for recording X-ray patterns of DNA with major components: X-ray source goniometer sample holder X-ray detector and/or plate holder;
  • 6 Illustrated animation of an X-ray goniometer;
  • 7 X-ray detector at the SLAC synchrotron facility;
  • 8 Neutron scattering facility at ISIS in UK;
    • Third and fourth rows: Molecular models of DNA structure at various scales; figure #11 is an actual electron micrograph of a DNA fiber bundle presumably of a single bacterial chromosome loop
File:Bragg diffractionpngFile:ABDNAxrgpjjpgFile:DNA in waterjpgFile:X ray diffractionpngFile:X Ray DiffractometerJPGFile:Kappa goniometer animationoggFile:SLAC detector edit1jpgFile:ISIS exptal halljpgFile:Dna-SNPsvgFile:DNA_replication_ensvgFile:DNA Under electron microscope Image 3576B-PHjpgFile:DNA Model Crick-WatsonjpgFile:DNA labelsjpgFile:AT DNA base pair ptsvgFile:A-B-Z-DNA Side ViewpngFile:Museo Príncipe Felipe ADNjpgFile:AGCT DNA minipngFile:BU Bio5jpgFile:Circular DNA SupercoilingpngFile:Rosalindfranklinsjokecardjpg

Paracrystalline lattice models of B-DNA structures

A paracrystalline lattice or paracrystalis a molecular or atomic lattice with significant amounts (eg larger than a few percent) of partial disordering of molecular arranegements Limiting cases of the paracrystal model are nanostructures such as glasses liquids etc that may possess only local ordering and no global orderLiquid crystals also have paracrystalline rather than crystalline structures
in 1952
Highly hydrated B-DNA occurs naturally in living cells in such a paracrystalline state which is a dynamic one in spite of the relatively rigid DNA double-helix stabilized by parallel hydrogen bonds between the nucleotide base-pairs in the two complementary helical DNA chains (see figures) For simplicity most DNA molecular models ommit both water and ions dynamically bound to B-DNA and are thus less useful for understanding the dynamic behaviors of B-DNA in vivo The physical and mathematical analysis of X-rayHosemann R., Bagchi RN Direct analysis of diffraction by matter North-Holland Publs Amsterdam – New York 1962 and spectroscopic data for paracrystalline B-DNA is therefore much more complicated than that of crystalline A-DNA X-ray diffraction patterns The paracrystal model is also important for DNA technological applications such as DNA nanotechnology Novel techniques that combine X-ray diffraction of DNA with X-ray microscopy in hydrated living cells are now also being developed (see for example "Application of X-ray microscopy in the analysis of living hydrated cells")

Genomic and Biotechnology Applications of DNA molecular modeling

The following gallery of images illustrates various uses of DNA molecular modeling in Genomics and Biotechnology research applications from DNA repair to PCR and DNA nanostructures; each slide contains its own explanation and/or details The first slide presents an overview of DNA applications including DNA molecular models with emphasis on Genomics and Biotechnology

Gallery: DNA Molecular modeling applications

File:Genomics GTL Pictorial ProgramjpgFile:RNA poljpgFile:Primase 3B39pngFile:Museo Príncipe Felipe ADNjpgFile:DNA RepairjpgFile:MGMT+DNA 1T38pngFile:DNA damaged by carcinogenic 2-aminofluorene AF jpgFile:A-DNA orbit animated smallgifFile:DNA labelsjpgFile:AT DNA base pair ptsvgFile:AGCT DNA minipngFile:A-B-Z-DNA Side ViewpngFile:BU Bio5jpgFile:Plasmid emNLjpgFile:Circular DNA SupercoilingpngFile:Chromatin chromosompngFile:ChromosomesvgFile:Chr2 orang humanjpgFile:3D-SIM-3 Prophase 3 colorjpgFile:Chromosome2 mergepngFile:Transkription Translation 01jpgFile:RibosomaleTranskriptionsEinheitjpgFile:Chromosome Conformation Capture TechnologyjpgFile:Mitochondrial DNA and diseasespngFile:PCRsvgFile:Pcr gelpngFile:DNA nanostructurespngFile:SFP discovery principlejpgFile:CdnaarrayjpgFile:Expression of Human Wild-Type and P239S Mutant PalladinpngFile:Random genetic drift chartpngFile:Co-dominance Rhododendronjpg

Databases for DNA molecular models and sequences

X-ray diffraction


Neutron scattering


X-ray microscopy


Electron microscopy


Atomic Force Microscopy (AFM)

Two-dimensional DNA junction arrays have been visualized by Atomic microscopy|Atomic Force Microscopy (AFM)] Other imaging resources for AFM/Scanning probe microscopy can be freely accessed at:

Gallery of AFM Images

File:DNA_nanostructurespngFile:Holliday junction colouredpngFile:Holliday Junction croppedpngFile:Atomic force microscope by ZureksjpgFile:Atomic force microscope block diagrampngFile:AFM view of sodium chloridegifFile:Single-Molecule-Under-Water-AFM-Tapping-ModejpgFile:AFMimageRoughGlass20x20png

Mass spectrometry--Maldi informatics

File:Maldi informatics figure 6JPG

Spectroscopy

  • Vibrational circular dichroism (VCD)
  • FT-NMR http://wwwjonathanpmillercom/Karplushtml- obtaining dihedral angles from 3J coupling constants http://wwwspectroscopynowcom/FCKeditor/UserFiles/File/specNOW/HTML%20files/General_Karplus_Calculatorhtm Another Javascript-like NMR coupling constant to dihedral
  • NMR microscopyLee S. C. et al (2001) One Micrometer Resolution NMR Microscopy J Magn Res 150: 207-213
  • Microwave spectroscopy
  • FT-IR
  • FT-NIRNear Infrared Microspectroscopy Fluorescence MicrospectroscopyInfrared Chemical Imaging and High Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds Somatic Embryos and Single Cells Baianu IC et al. 2004 In Oil Extraction and Analysis D. Luthria Editor pp241-273 AOCS Press Champaign ILSingle Cancer Cell Detection by Near Infrared Microspectroscopy Infrared Chemical Imaging and Fluorescence Microspectroscopy2004I C. Baianu D. Costescu N. E. Hofmann and S. S. Korban q-bio/0407006 (July 2004)Raghavachari R., Editor 2001 Near-Infrared Applications in Biotechnology Marcel-Dekker New York NY
  • Spectral Hyperspectral and Chemical imaging)http://wwwimagingnet/chemical-imaging/ Chemical imaginghttp://wwwmalverncom/LabEng/products/sdi/bibliography/sdi_bibliographyhtm E. N. Lewis E. Lee and L. H. Kidder Combining Imaging and Spectroscopy: Solving Problems with Near-Infrared Chemical Imaging Microscopy Today Volume 12, No. 6, 11/2004DS Mantus and G. H. Morrison 1991 Chemical imaging in biology and medicine using ion microscopy Microchimica Acta 104 (1-6) January 1991 doi: 101007/BF01245536Near Infrared Microspectroscopy Fluorescence MicrospectroscopyInfrared Chemical Imaging and High Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds Somatic Embryos and Single Cells Baianu IC et al. 2004 In Oil Extraction and Analysis D. Luthria Editor pp241-273 AOCS Press Champaign ILSingle Cancer Cell Detection by Near Infrared Microspectroscopy Infrared Chemical Imaging and Fluorescence Microspectroscopy2004I C. Baianu D. Costescu N. E. Hofmann and S. S. Korban q-bio/0407006 (July 2004)J Dubois G. Sando E. N. Lewis Near-Infrared Chemical Imaging A Valuable Tool for the Pharmaceutical Industry GIT Laboratory Journal Europe No1-2 2007Applications of Novel Techniques to Health Foods Medical and Agricultural Biotechnology(June 2004)I C. Baianu P. R. Lozano V. I. Prisecaru and H. C. Lin q-bio/0406047
  • Raman spectroscopy/microscopy Chemical Imaging Without Dyeing and CARSCL Evans and XS Xie2008 Coherent Anti-Stokes Raman Scattering : Chemical Imaging for Biology and Medicine doi:101146/annurevanchem1031207112754 Annual Review of Analytical Chemistry 1: 883-909
  • Fluorescence correlation spectroscopyEigen M., Rigler M. Sorting single molecules: application to diagnostics and evolutionary biotechnology(1994) Proc Natl Acad Sci USA 915740-5747Rigler M. Fluorescence correlations single molecule detection and large number screening Applications in biotechnology(1995) J. Biotechnol 41177-186Rigler R. and Widengren J. (1990) Ultrasensitive detection of single molecules by fluorescence correlation spectroscopy BioScience (Ed Klinge & Owman) p180Single Cancer Cell Detection by Near Infrared Microspectroscopy Infrared Chemical Imaging and Fluorescence Microspectroscopy2004I C. Baianu D. Costescu N. E. Hofmann S. S. Korban and et al q-bio/0407006 (July 2004)Oehlenschläger F., Schwille P. and Eigen M. (1996) Detection of HIV-1 RNA by nucleic acid sequence-based amplification combined with fluorescence correlation spectroscopy Proc Natl Acad Sci USA 93:1281Bagatolli LA and Gratton E. (2000) Two-photon fluorescence microscopy of coexisting lipid domains in giant unilamellar vesicles of binary phospholipid mixtures Biophys J., 78:290-305Schwille P., Haupts U., Maiti S., and Webb W(1999) Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one- and two-photon excitation Biophysical Journal 77(10):2251-2265Near Infrared Microspectroscopy Fluorescence MicrospectroscopyInfrared Chemical Imaging and High Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds Somatic Embryos and Single Cells Baianu IC et al. 2004 In Oil Extraction and Analysis D. Luthria Editor pp241-273 AOCS Press Champaign IL Fluorescence cross-correlation spectroscopy and FRET FRET description doi:101016/S0959-440X(00)00190-1Recent advances in FRET: distance determination in protein–DNA complexes Current Opinion in Structural Biology 2001 11(2) 201-207 http://wwwfretimagingorg/mcnamaraintrohtml FRET imaging introduction
  • Confocal microscopyEigen M., and Rigler R. (1994) Sorting single molecules: Applications to diagnostics and evolutionary biotechnology Proc Natl Acad Sci USA 91:5740

Gallery: CARS (Raman spectroscopy) Fluorescence confocal microscopy and Hyperspectral imaging

File:Stokes shiftpngFile:CARS SchemesvgFile:HyperspectralCubejpgFile:MultispectralComparedToHyperspectraljpgFile:ConfocalprinciplesvgFile:3D-SIM-1 NPC Confocal vs 3D-SIM detailjpgFile:TirfmsvgFile:Inverted microscopejpgFile:Fluorescence microscopjpgFile:Microscope And Digital CameraJPGFile:FluorescenceFilters 2008-09-28svgFile:FluorescentCellsjpgFile:Yeast membrane proteinsjpgFile:S cerevisiae septinsjpgFile:Dividing Cell FluorescencejpgFile:HeLa Hoechst 33258jpgFile:FISH 13 21jpg
File:Bloodcell sun flares pathologyjpegFile:Carboxysome 3 imagespng

Genomic and structural databases


Notes

References

  • Applications of Novel Techniques to Health Foods Medical and Agricultural Biotechnology(June 2004) I. C. Baianu P. R. Lozano V. I. Prisecaru and H. C. Lin q-bio/0406047
  • F. Bessel Untersuchung des Theils der planetarischen Störungen Berlin Abhandlungen (1824) article 14
  • Sir Lawrence Bragg FRS The Crystalline State A General survey : G. Bells and Sons Ltd vols 1 and 2., 1966 2024 pages
  • Cantor C. R. and Schimmel PR Biophysical Chemistry Parts I and II San Franscisco: WH Freeman and Co. 1980 1800 pages
  • Eigen M., and Rigler R. (1994) Sorting single molecules: Applications to diagnostics and evolutionary biotechnology Proc Natl Acad Sci USA 91:5740
  • Raghavachari R., Editor 2001 Near-Infrared Applications in Biotechnology Marcel-Dekker New York NY
  • Rigler R. and Widengren J. (1990) Ultrasensitive detection of single molecules by fluorescence correlation spectroscopy BioScience (Ed Klinge & Owman) p180
  • Single Cancer Cell Detection by Near Infrared Microspectroscopy Infrared Chemical Imaging and Fluorescence Microspectroscopy2004 I. C. Baianu D. Costescu N. E. Hofmann S. S. Korban and et al q-bio/0407006 (July 2004)
  • Voet D. and JG Voet Biochemistry 2nd Edn New York Toronto Singapore: John Wiley & Sons Inc 1995 ISBN 0-471-58651-X 1361 pages
  • Watson G. N. A Treatise on the Theory of Bessel Functions (1995) Cambridge University Press ISBN 0-521-48391-3
  • Watson James D. and Francis HC Crick A structure for Deoxyribose Nucleic Acid (PDF) Nature 171 737–738 25 April 1953
  • Watson James D. Molecular Biology of the Gene New York and : WA Benjamin Inc 1965 494 pages
  • Wentworth WE Physical Chemistry A short course Malden (Mass): Blackwell Science Inc 2000
  • Herbert R. Wilson FRS Diffraction of X-rays by proteins Nucleic Acids and Viruses : Edward Arnold (Publishers) Ltd 1966
  • Kurt Wuthrich NMR of Proteins and Nucleic Acids New York BrisbaneChicester Toronto Singapore: J. Wiley & Sons 1986 292 pages
  • Link

See also


External links




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