This is a course on the 3-dimensional molecular structure of biological macromolecules, particularly nucleic acids. The course will emphasize an understanding of the principles involved in the description, elucidation and crystallographic determination of 3-D structure.


Students will be graded on a written paper based on The Eighth Day of Creation by Horace F. Judson, 1 or 2 exams, on an oral presentation of a paper on an assigned topic from the recent literature, and on their contributions to the discussions of the presentations by other students. The relative weights are: Paper, 2; Exam 1, 3; Presentation, 2; Discussion 1; Exam 2, if given, 2.

For the paper, in each section of the book, choose a major example of the prevailing wisdom that was incorrect before the work described was performed. Show the basis of the fallacies and explain the experiments that eventually overturned them. Read the entire book first. The paper should be about 10 pages double spaced.

Papers that are late, are not typed, or are not spell-checked and grammar-checked are not acceptable.


The following topics will be covered, as time permits:

The Description of Structure

Coordinates, coordinate systems, transformations of coordinates, and quantities derived from coordinates, such as distances, angles, torsion angles.


Symmetry of biological molecules, viruses, and crystals; helices, point groups and space groups.

Introduction to X-ray Crystallography

Scattering, Fourier transforms, reciprocal space and resolution.

Components of Macromolecular Structure

Hydrogen bonding, base stacking and hydrophobics, paired interactions, backbone torsion angle classes, solvent interactions, secondary structures.

Details of Observed Structures

B, A, Z-DNA helices, RNA helices, tRNA structure, DNA supercoiling, topology, and intercalation; protein-nucleic acid interactions.

Structural DNA Nanotechnology

Derivation of motifs, sequence design, objects, devices, periodic arrays, relationship to DNA-based computation.

Homepage for Macromolecular Chemistry, 2005

Homepage for Ned Seeman's Lab