DNA PACKING:

Distances Between

DNA Moleculesin Crystals

Bryson W. Finklea

St. John's College

DIMACS REU

Unit Cell

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

NDB #: bdl042 (Rasmol images) Space Group: C 2

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

NDB #: bdl042 (Rasmol images) Space Group: C 2

NDB #: adh007

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

(Rasmol images) Space Group: P 61

NDB #: adh007

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

(Rasmol images) Space Group: P 61

Example of 2D symmetry in a

wallpaper pattern

To show symmetry:

●pick a point

●find all equivalent points

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

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

Generalized 3D unit cell—a parallelepiped

3D Symmetry

(Unknown)

http://www.chem.ox.ac.uk/icl/heyes/structure_of_solids/Lecture1/Bravais.gif

Categories of Space Groups

Proper symmetry elements in 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 elements in 3D:•Reflection planes•Glide reflection planes (reflection and translation)•Inversion points•Rotary inversion axes (rotation and inversion)

Symmetry operations –the actual changes carried outin relation to a symmetry element

Sets of symmetry operations form algebraic groups calledspace groups.

•230 space groups

Space Group Total Total w/ DNA DNA DNAEntries Res<2.0 only complexes Total

C 1 2 1 135 67 17 75 92P 21 21 21 476 222 126 324 450H 3 24 10 5 15 2052 Others 984 317 164 534 698

54 (of 230) Total 1619 616 312 948 1260

Asymmetric Unit Unit Cell 3x3x3 Block of Unit Cells

NDB #: bdl042 (Rasmol images) Space Group: C 2

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

My Project

Example output from programof distances less than 3.0 angstroms:

(for bdl042.pdb)

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

NanotechnologyNature

Background

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

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

Acknowledgments

DIMACS REUNSF 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)