Course Description

The building of space filling models to help students understand the structure/function relationships of RNA and DNA. Computer modeling approaches will also be taught.

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Athena Title

DNA MODELING

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Semester Course Offered

Offered fall

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Grading System

A - F (Traditional)

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Course Objectives

Using CPK models, students will learn the nomenclature of nucleic acids and their substituents, assemble nucleotides and assemble them into a variety of DNA structures. As a group project, the class will assemble a single transfer RNA and solve the three dimensional structure of its anticodon U-turn. Finally, students will learn how to use a variety of programs to assemble specific DNA sequences and proteins as well as how to dock proteins onto DNA sequences. The learning outcome is a deep understanding of three-dimensional structures of nucleic acids and how they interact with proteins in structure/function relationships.

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Topical Outline

Nomenclature of nucleic acids Assemble all four nucleotide monophosphates and link into a 5’->3’ tetramer (pGpApTpC) Base-pairing: standard Watson & Crick vs nonstandard basepairing Assemble A:T and G:C into B-DNA: sugar phosphate backbone and angles of rotation Assemble a long B DNA molecule of defined sequence (class project) Assemble four G:C basepairs into Z-DNA (work in pairs) Assemble a G:C quartet: Hoogsteen basepairing Assemble yeast tRNAphe (class project) Assemble anticodon U-turn Basic computer programs to assemble B DNA of defined sequence as well as building a DNA binding protein (e.g., lac repressor) from the database Docking the repressor onto the operator site The course syllabus is a general plan for the course; deviations announced to the class by the instructor may be necessary.

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