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DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John\'s College

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DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John\'s College DIMACS REU. Outline: Background Symmetry My Project. Outline: Background Symmetry My Project. Background. Different representations of the same DNA

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slide1

DNA PACKING:

Characterizing

Intermolecular Contacts

of DNA

Bryson W. Finklea

St. John\'s College

DIMACS REU

slide2

Outline:

  • Background
  • Symmetry
  • My Project
slide3

Outline:

  • Background
  • Symmetry
  • My Project
slide4

Background

Different representations of the same DNA

(18 base pairs color-coded according to base identity)

(http://siggy.chem.ucla.edu/~tim/chemistry/DNA.jpg)

slide5

Background

In nature each human cell has

3 billion DNA base pairs

(about 2 meters long)

(Human Genome Project Information of the DOE)

slide6

Background

In nature each human cell has

3 billion DNA base pairs

(about 2 meters long)

Cube built from DNA

in nanotechnology lab

(Human Genome Project Information of the DOE) (Dr. Nadrian Seeman, Department of Chemistry,

New York University)

slide7

Background

Molecular Crystals

(often microscopic)*

(www.scripps.edu/newsandviews/e_20010129/chang-2.html)

*These are similar examples from proteins instead of DNA.

slide8

Background

Molecular Crystals

(often microscopic)*

DNA X-Ray Diffraction Pattern*

(www.scripps.edu/newsandviews/e_20010129/chang-2.html)

(http://userpage.chemie.fu-berlin.de/~psf/ifv_psfx.htm)

*These are similar examples from proteins instead of DNA.

slide9

Outline:

  • Background
  • Symmetry
  • My Project
slide10

3D Symmetry

  • Crystal –
  • a solid with regularly repeating arrangement of atomsUnit Cell –
  • the basic unit of symmetry
  • an arrangement of atoms
  • that repeats in every direction

(Unknown)

slide11

Example of 2D symmetry in a

wallpaper pattern

(http://www.clarku.edu/~djoyce/wallpaper/)

slide12

Example of 2D symmetry in a

wallpaper pattern

To show symmetry:

  • pick a point
slide13

Example of 2D symmetry in a

wallpaper pattern

To show symmetry:

  • pick a point
  • find all equivalent points
slide14

Example of 2D symmetry in a

wallpaper pattern

To show symmetry:

  • pick a point
  • find all equivalent points
  • the points form a 2D lattice
slide15

Example of 2D symmetry in a

wallpaper pattern

  • Connecting 4 lattice points to form a parallelogram gives a possible unit cell
  • Unit cell – the basic unit that repeats in every direction
  • Different unit cells can be chosen
  • But some unit cells are preferable for higher symmetry
slide16

3D Symmetry

  • Symmetry is defined bysymmetry elements
  • Four possible symmetry elements in 2D:
  • Rotation points (by 60°, 90°, 120°, or 180°)
  • Reflection axes
  • Glide reflection axes (reflection and translation)
  • Inversion points
  • (Translation)
  • Symmetry operations –the actual changes carried out
  • in relation to a symmetry element
slide17

Example of 2D symmetry in a

wallpaper pattern

Reflection Axis

Glide Reflection Axis

90° Rotation Point

180° Rotation Point

Symmetry elements of this wallpaper group

(http://www.clarku.edu/~djoyce/wallpaper/)

slide18

Example of 2D symmetry in a

wallpaper pattern

  • Unit cell

Reflection Axis

Glide Reflection Axis

90° Rotation Point

180° Rotation Point

Symmetry elements of this wallpaper group

slide19

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

slide20

3D Symmetry

Generalized 3D unit cell—a parallelepiped

(Unknown)

slide21

3D Symmetry

  • Crystal –
  • a solid with regularly repeating arrangement of atomsUnit Cell –
  • the basic unit of symmetry
  • an arrangement of atoms
  • that repeats in every direction
  • (Different colors are different copies of the same asymmetric unit)
slide22

3D Symmetry

  • Six symmetry elementsin 3D:
  • Rotation axes (by 60°, 90°, 120°, or 180°)
  • Reflection planes
  • Glide reflection planes (reflection and translation)
  • Inversion points
  • (Translation)
  • Screw Axes (translation and rotation)
  • Rotary inversion axes (rotation and inversion)
  • Sets of symmetry operations form algebraic groups called
  • space groups.
  • 230 space groups
slide23

3D Symmetry

Asymmetric unit Unit cell 27 adjacent unit cells

slide24

Outline:

  • Background
  • Symmetry
  • My Project
slide25

My Project

Characterizing Intermolecular Contacts of DNA

Data from Nucleic Acid Database (NDB):

  • orthogonal coordinates of atoms in an asymmetric unit
  • 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
  • make measurements of interesting properties of contacts between

molecules of DNA (Examples: distances, angles between axes,…)

slide26

3D Symmetry

Asymmetric unit Unit cell 27 adjacent unit cells

slide27

Final Presentation:

  • Details on computer program structure

and images created using its output

  • Specification of important DNA molecular contacts

and report of findings

  • Perhaps more details on mathematics of space groups, including notation used
slide28

References:

DNA for the layman:

Understanding DNA, Calladine and Drew, 3rd edition.

Symmetry in crystals, including space group theory:

Crystal Structure Analysis for Chemist and Biologists, Glusker, et al, Ch. 1, 2, and 4.

X-Ray Analysis and the Structure of Organic Molecules,

Dunitz, Ch. 2.

Molecular structure databases (on web):

Nucleic Acid Database (NDB), Protein Data Bank (PDB),

Cambridge Structural Database (CSB)

slide29

Acknowledgments

DIMACS REU

NSF Support

Advisor:

Wilma Olson, Department of Chemistry,

Rutgers University

Additional Advisors:

A.R. Srinivasan, Department of Chemistry

Rutgers University

Andrew Colasanti, Department of Molecular Biology

Rutgers University

(background: http://www.karolinskaeducation.ki.se/services/courses/selection_courses_se.html)

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