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DNA PACKING: Distances Between DNA Molecules in Crystals Bryson W. Finklea St. John's College DIMACS REU

DNA PACKING: Distances Between DNA Molecules in Crystals Bryson W. Finklea St. John's College DIMACS REU. Unit Cell . Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells.

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DNA PACKING: Distances Between DNA Molecules in Crystals Bryson W. Finklea St. John's College DIMACS REU

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  1. DNA PACKING: Distances Between DNA Molecules in Crystals Bryson W. Finklea St. John's College DIMACS REU

  2. Unit Cell

  3. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

  4. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells (Rasmol images) Space Group: C 2 NDB #: bdl042

  5. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells (Rasmol images) Space Group: C 2 NDB #: bdl042

  6. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells (Rasmol images) Space Group: P 61 NDB #: adh007

  7. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells (Rasmol images) Space Group: P 61 NDB #: adh007

  8. Example of 2D symmetry in a wallpaper pattern To show symmetry: • pick a point • find all equivalent points

  9. Example of 2D symmetry in a wallpaper pattern • Connecting 4 lattice points in a parallelogram gives a unit cell • Unit cell – the basic unit that repeats in every direction • Some unit cells are conventionally used because of their higher symmetry

  10. Example of 2D symmetry in a wallpaper pattern • Unit cell* • Asymmetric Unit –the simplest unit on which the symmetry operations can act to produce the entire symmetrical structure* Reflection Axis Glide Reflection Axis 90° Rotation Point 180° Rotation Point Symmetry elements of this wallpaper group * Although the spirit of what I show is correct, it appears from the following website that my choice of conventional unit cell and choice of asymmetric unit may be unconventional or even wrong. See the last example in the n=4 section of the following website: http://jwilson.coe.uga.edu/EMT668/EMAT6680.F99/McCallum/WALLPA~1/SEVENT~1.HTM

  11. 3D Symmetry Generalized 3D unit cell—a parallelepiped (Unknown)

  12. Categories of Space Groups http://www.chem.ox.ac.uk/icl/heyes/structure_of_solids/Lecture1/Bravais.gif

  13. Proper symmetry elementsin 3D: • Rotation axes (by 60°, 90°, 120°, or 180°) • Notated: 6, 4, 3, and 2, respectively • Screw Axes (translation and rotation) • Notated: 61, 62, 63, 64, 65; 41, 42, 43; 31, 32; and 21 • (Translation) • Proper symmetry elementsin 3D: • Reflection planes • Glide reflection planes (reflection and translation) • Inversion points • Rotary inversion axes (rotation and inversion)

  14. Symmetry operations –the actual changes carried out • in relation to a symmetry element • Sets of symmetry operations form algebraic groups called • space groups. • 230 space groups

  15. Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells (Rasmol images) Space Group: C 2 NDB #: bdl042

  16. My Project Characterizing Intermolecular Contacts of DNA Data from Nucleic Acid Database (NDB): • orthogonal coordinates of atoms in asymmetric unit • conversion matrix from orthogonal to fractional (unit cell) coordinates • equivalent positions in equation form (info from symmetry elements) • unit cell dimensions and angles To revise a computer program to: • reconstruct coordinates of the atoms in a unit cell • …then in a 3x3x3 block of unit cells • Measure distances between pairs of atoms in different molecules

  17. UCELL MOL AT# AT RES UCELL MOL AT# AT RES DISTANCE 0. 0. 0. 1 216 O2 C 0. 0. 0. 2 227 C4* G 2.93 0. 0. 0. 1 227 C4* G 0. 0. 0. 2 216 O2 C 2.93 0. 0. 0. 1 240 C2 G 0. 0. 0. 2 288 O4* T 2.95 0. 0. 0. 1 264 C5* G 0. 0. 0. 2 264 C5* G 2.96 0. 0. 0. 1 288 O4* T 0. 0. 0. 2 240 C2 G 2.95 0. 0. 0. 1 19 O2P G 1. 0. 1. 2 19 O2P G 2.75 0. 0. 0. 1 37 N3 G 1. 0. 1. 2 484 N2 G 2.98 0. 0. 0. 1 452 O4* C 1. 0. 1. 2 473 O3* G 2.62 0. 0. 0. 1 454 O3* C 1. 0. 1. 2 469 C5* G 2.67 0. 0. 0. 1 469 C5* G 1. 0. 1. 2 454 O3* C 2.67 0. 0. 0. 1 469 C5* G 1. 0. 1. 2 469 C5* G 2.28 0. 0. 0. 1 471 O4* G 1. 0. 1. 2 471 O4* G 2.55 0. 0. 0. 1 473 O3* G 1. 0. 1. 2 452 O4* C 2.62 0. 0. 0. 1 484 N2 G 1. 0. 1. 2 37 N3 G 2.98 0. 0. 0. 1 484 N2 G 1. 0. 1. 2 484 N2 G 2.73 0. 0. 0. 2 19 O2P G -1. 0.-1. 1 19 O2P G 2.75 0. 0. 0. 2 37 N3 G -1. 0.-1. 1 484 N2 G 2.98 0. 0. 0. 2 452 O4* C -1. 0.-1. 1 473 O3* G 2.62 0. 0. 0. 2 454 O3* C -1. 0.-1. 1 469 C5* G 2.67 0. 0. 0. 2 469 C5* G -1. 0.-1. 1 454 O3* C 2.67 0. 0. 0. 2 469 C5* G -1. 0.-1. 1 469 C5* G 2.28 0. 0. 0. 2 471 O4* G -1. 0.-1. 1 471 O4* G 2.55 0. 0. 0. 2 473 O3* G -1. 0.-1. 1 452 O4* C 2.62 0. 0. 0. 2 484 N2 G -1. 0.-1. 1 37 N3 G 2.98 0. 0. 0. 2 484 N2 G -1. 0.-1. 1 484 N2 G 2.73 Example output from program of distances less than 3.0 angstroms: (for bdl042.pdb)

  18. Background Nature Nanotechnology (Human Genome Project Information of the DOE) (Dr. Nadrian Seeman, Department of Chemistry, New York University)

  19. Future Work: • Tweak output features of program • Run program on all DNA-only files of NDB • Characterize intermolecular contacts in different ways e.g. angle between DNA molecular axes • Alter notation of program to run it on NDB files containing RNA, protein, and drug molecules

  20. Acknowledgments DIMACS REU NSF Support Advisor: Wilma Olson, Department of Chemistry, Rutgers University Additional Advisor: A.R. Srinivasan, Department of Chemistry, Rutgers University (background: http://www.karolinskaeducation.ki.se/services/courses/selection_courses_se.html)

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