History of Biophysics 101

  • Taught in 1988, 1990, 1992, 1994, 1996 & 1998 as Genetics 210 "Conceptual Foundations of DNA Research" by George Church and Brian Seed.
  • In 1997 called Biophysics 242 "Special Topics in Biophysics"
  • In 1999 called Biophysics 101 "Genomics and Computational Biology" saw introduction of web accessible PPT lectures by George Church, Tim Chen, Tao Wei, Jeremy Edwards, and Bob Freeman (One TF, Dan Janse).
  • In 2000, It switched to a format enabling "distance learning" (i.e. streaming web video with interlaced ppt), one lecturer, 8 sections (through 2003).
  • In 2001 also listed as MIT-HST 508.
  • In 2002 also listed as Medical Sciences - Genetics 224.
  • In 2002 Fall it became one of the first MIT experiments in Open Course-Ware (OCW).
  • In 2003 the full web site is replicated here (last year of 2000-2003 Harvard-DCE option).
  • In 2005, The title changed to "Genomics, Computing, Economics, and Society" and the format changed to more emphasis on a team project and class discussion. (MIT course # changed to HST.510)
  • In 2007 Changed back to " Genomics & Computational Biology" Project: Trait-o-matic: going from full human genome sequence to traits.
  • In 2009 Fall -- see Wiki Project on genome interpreation and personalized medicine.

    1988 Syllabus for Genetics 210. Conceptual Foundations for DNA Research

    I. Three dimensional images: from chromosomes to base-pairs

      A. Microscopy and spectroscopy
      B. Crystallography and molecular dynamics

    II. Structures: symmetry and recognition

      A.  A, B, Z, H, bent, kinked, ss DNA propellor twist, hydrogen bonds, base stacking, syn-anti
      B. ds RNA, tRNA, non Watson-Crick base pairs, mismatches
      C. Solvent, metal interactions
      D. EcoRI-DNA complex

    III. Inter- and intra-molecular interactions of DNA as a polymer, cooperativity, "nonspecific" interactions

      A. Equilibrium thermodynamics, helix-coil, secondary structure
      B. Kinetics, diffusion
      C. Electrophoresis, field inversion, gel retardation
      D. Hybridization, Tm, kinetics, detection limits
      E. Sedimentation, circle topology, ligation
      F. Cloning theory, representation

    IV. Chemistry

      A. Mutagenesis, photochemistry
      B. Fluorescence, FACS
      C. DNA synthesis, uses of analogs
      D. Restriction mapping
      E. DNA sequencing, PCR, modified bases, footprinting, conformational probes, S1
      F. Active sites of nucleic acids, tRNA-Pb, telomeres

    V. Similar and homologous sequences and 3D structures, evolutionary considerations

    VI. DNA-protein complexes

      A. TFIIIA, rec1, PolI, CAP, fd gene5
      B. DBII, nucleosomes, chromosomes, research frontiers