BCHM 660 - Nucleic Acids
FALL 2007

Course Homepage

Instructors: Joe Ogas
ogas@purdue.edu

Fred Gimble
fgimble@purdue.edu

Lee Weith
weith@purdue.edu

Office Hours: by appointment
TA: Hajeong Kim
kim95@purdue.edu
Office Hours: Tuesdays, 2-4pm, BCHM 320
Topics scheduled to be covered by Joe Ogas (8/20 – 9/7):
  • Nucleic acid structure (chemistry and structure)
  • DNA replication, transcription by polymerases: structure, mechanism of polymerases,
  • Reverse transcriptase, telomerase/telomeres
  • DNA damage and repair
  • Molecular biology techniques involving nucleic acids – Sequencing, restriction enzymes, ligases,
  • PCR (emphasis on quantitative)
  • Histones, chromatin structure and remodeling (includes analysis of paper)
Topics scheduled to be covered by Lee Weith (9/10,14,17,21):
  • secondary structure of RNA; predictions; footprinting
  • RNA splicing
  • catalytic RNA
  • Protein-RNA recognition
Topics scheduled to be covered by Fred Gimble (9/12,19):
  • How DNA-binding proteins locate their targets
  • General strategies used by DNA-binding proteins for interacting with DNA(van der Waals contacts, hydrogen bonding, ionic interactions and water-mediated bonds)
  • Direct and indirect readout mechanisms
  • Protein-induced DNA distortion
  • Classes of DNA-binding motifs and their properties
  • Methods to study protein-DNA interactions (including DNA footprinting, EMSA, Biacore, and single-molecule analyses) and their advantages and drawbacks
Final Exam: 9/25 7-9pm WTHR 172
Grades will be based on problem set (20%) and the final exam (80%). No late problem
sets will be accepted for any reason.

Reserve Material (Life Sciences Library in Lilly Hall):
Class Handouts
Principles of Nucleic Acid Structure – Wolfram Saenger
DNA Structure and Function - Richard Sinden
The RNA World – Gesteland, Cech, Atkins, eds
Introduction to Protein Structure – Branden and Tooze

For a Printer-friendly version of all the above information, please click here (BCHM 660 2007 syllabus.pdf - 38 KB).


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