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

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