Campuses:

Sequence-Dependent Helical Structure and Global Responses of DNA Part I.<br/><br/>

Saturday, September 15, 2007 - 9:00am - 10:00am
EE/CS 3-180
Wilma Olson (Rutgers, The State University of New Jersey)
(Towards understanding the processing and packaging of genetic
information at the molecular level)


Part I. Information content in known three-dimensional structures
of nucleic acids: sequence-dependent conformation, deformation,
interactions


    A. The classic B-DNA double helix: Watson-Crick base pair
    side groups vs. the polyanionic sugar-phosphate backbone


    B. DNA phase transitions and RNA double helices



  1. The A/B double helical transition and DNA bending
    Structural discriminants of A vs. B DNA
    Protein-induced A/B transitions


  2. The B/C double helical transition and DNA packaging
    Nucleosome core particle: a striking example of protein-induced
    DNA deformation via concerted changes in kinking and base-pair
    displacement
    Tight bending of DNA via B→A and B→C helical transitions

  3. The A-RNA double helix, including non-canonical base
    pairs


C. Chemical basis of DNA sequence-dependent properties:
structure, deformability, recognition


  1. Indirect (electrostatic) mechanism of nucleosomal DNA folding
    vs. sequence-dependent character of known positioning sequences

  2. Indirect recognition of sequences: pyrimidine-purine
    base-pair steps as sites of DNA deformability

  3. Patterns of base-amino acid contacts: direct recognition of
    specific DNA sequences by proteins

  4. DNA electrostatics, amino acid binding propensities,
    intrinsic curvature

  5. Recognition and structural roles of non-canonical base pairs


MSC Code: 
92D20