dna packing: characterizing intermolecular contacts of dna bryson w. finklea st. john's college...
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![Page 1: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/1.jpg)
DNA PACKING:
Characterizing Intermolecular
Contacts of DNA
Bryson W. Finklea
St. John's College
DIMACS REU
![Page 2: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/2.jpg)
Outline:
● Background
● Symmetry
● My Project
![Page 3: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/3.jpg)
Outline:
● Background
● Symmetry
● My Project
![Page 4: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/4.jpg)
Different representations of the same DNA(18 base pairs color-coded according to base identity)
Background
(http://siggy.chem.ucla.edu/~tim/chemistry/DNA.jpg)
![Page 5: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/5.jpg)
In nature each human cell has 3 billion DNA base pairs
(about 2 meters long)
Background
(Human Genome Project Information of the DOE)
![Page 6: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/6.jpg)
Cube built from DNAin nanotechnology lab
In nature each human cell has 3 billion DNA base pairs
(about 2 meters long)
Background
(Human Genome Project Information of the DOE) (Dr. Nadrian Seeman, Department of Chemistry, New York University)
![Page 7: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/7.jpg)
Background
Molecular Crystals(often microscopic)*
(www.scripps.edu/newsandviews/e_20010129/chang-2.html)
*These are similar examples from proteins instead of DNA.
![Page 8: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/8.jpg)
DNA X-Ray Diffraction Pattern*
Background
Molecular Crystals(often microscopic)*
(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.
![Page 9: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/9.jpg)
Outline:
● Background
● Symmetry
● My Project
![Page 10: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/10.jpg)
Crystal – a solid with regularly repeating arrangement of atoms
Unit Cell – •the basic unit of symmetry•an arrangement of atoms that repeats in every direction
3D Symmetry
(Unknown)
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Example of 2D symmetry in a
wallpaper pattern
(http://www.clarku.edu/~djoyce/wallpaper/)
![Page 12: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/12.jpg)
Example of 2D symmetry in a
wallpaper pattern
To show symmetry:
●pick a point
![Page 13: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/13.jpg)
Example of 2D symmetry in a
wallpaper pattern
To show symmetry:
●pick a point
●find all equivalent points
![Page 14: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/14.jpg)
Example of 2D symmetry in a
wallpaper pattern
To show symmetry:
●pick a point
●find all equivalent points
●the points form a 2D lattice
![Page 15: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/15.jpg)
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
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Symmetry is defined by symmetry 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 outin relation to a symmetry element
3D Symmetry
![Page 17: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/17.jpg)
Symmetry elements of this wallpaper group
Reflection Axis
Glide Reflection Axis
90° Rotation Point
180° Rotation Point
Example of 2D symmetry in a
wallpaper pattern
(http://www.clarku.edu/~djoyce/wallpaper/)
![Page 18: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/18.jpg)
Symmetry elements of this wallpaper group
Reflection Axis
Glide Reflection Axis
90° Rotation Point
180° Rotation Point
Example of 2D symmetry in a
wallpaper pattern
●Unit cell
![Page 19: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/19.jpg)
Symmetry elements of this wallpaper group
Reflection Axis
Glide Reflection Axis
90° Rotation Point
180° Rotation Point
●Asymmetric Unit –the simplest unit on which the symmetry operations can act to produce the entire symmetrical structure*
Example of 2D symmetry in a
wallpaper pattern
●Unit cell*
* 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
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Generalized 3D unit cell—a parallelepiped
3D Symmetry
(Unknown)
![Page 21: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/21.jpg)
3D Symmetry
Crystal – a solid with regularly repeating arrangement of atoms
Unit 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)
![Page 22: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/22.jpg)
Six symmetry elements in 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 calledspace groups.
•230 space groups
3D Symmetry
![Page 23: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/23.jpg)
Asymmetric unit Unit cell 27 adjacent unit cells
3D Symmetry
![Page 24: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/24.jpg)
Outline:
● Background
● Symmetry
● My Project
![Page 25: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/25.jpg)
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,…)
My Project
![Page 26: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/26.jpg)
Asymmetric unit Unit cell 27 adjacent unit cells
3D Symmetry
![Page 27: DNA PACKING: Characterizing Intermolecular Contacts of DNA Bryson W. Finklea St. John's College DIMACS REU](https://reader030.vdocuments.mx/reader030/viewer/2022032521/56649d5e5503460f94a3e08b/html5/thumbnails/27.jpg)
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
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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)
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Acknowledgments
DIMACS REUNSF Support
Advisor:
Wilma Olson, Department of Chemistry,
Rutgers University
Additional Advisors:
A.R. Srinivasan, Department of Chemistry
Rutgers University
Andrew Colasanti, Department of Molecular BiologyRutgers University(background: http://www.karolinskaeducation.ki.se/services/courses/selection_courses_se.html)