Partial
Reading List-Fall 2010
BIO 401/501
NOTE: Not all these papers will be assigned. This list is also incomplete, additional papers may be assigned. See also UBLearns site for this course!
Reference Book
Principles of Nucleic Acid Structure by Wolfram Saenger. (on reserve in library)
Journal Articles
Base Stacking
Wang & Kool, Biochemistry (1995), 34, 4125-4132
Freier,
et al. Biochemistry 1983, 22, 6198-6206
Matray & Kool JACS (1998) 120 6191-2
DNA Structure
Dickerson,
et al. (1982) Science 216, 475-485.
Vargason,
et al. (2001) Proc. Natl. Acad Sci. USA 98,
7265-7270
See the Movies! Helix
Basepair
Dickerson, R.E.,
& Ng, H.-L., (2002) Proc. Natl. Acad Sci. USA 98,
6986-6988
Protein-DNA Interactions
DNA
Sequence specific binding overview
DNA
sequence determinants for CAP binding
Chain Behavior
Shore et al., (1981) PNAS 78, 4833-4837
Taylor, W.H. and Hagerman. P.J. (1990) J. Mol. Biol. 212, 363-376.
Transcriptionally-Induced Supercoiling
Tsao, et al. (1989) Cell 56, 111-118.
Nucleosomes
Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986).
Sequence
periodicities in chicken nucleosome core
DNA. J. Mol.
Biol. 191, 659–675.
Buttinelli et al PNAS (1998) 95; 8544-8549
Richmond & Davey Nature (2003) 423, 145-150
Widlund et al. J. Mol. Biol. (1997) 267, 807-817
Luger, et al. NATURE (1997) 389, 251-260
ThaÊ stro Èm, et al. J. Mol. Biol. (1999) 288, 213-229
Sequence-Induced DNA Bending
Koo, et al. (1986) Nature 320, 501-506.
Nelson et al. (1987) Nature 330, 221-226.
Gartenberg et al. (1988) Nature 333, 824-829.
Howerton, et al. (2001) Biochemistry 40, 10023-31
Maki, et. al. (2003) Nucl. Acids Res. 31 1059-1066
Protein-DNA Interactions
Parkinson, et al. (1996) Journal of Molecular Biology 260, p 395-408 (Adobe-PDF)
Gunasekera A, Ebright YW, Ebright RH (1992) J Biol Chem; 267(21):14713-20
RNA Structure and Protein-RNA Interactions
Rould, et al. (1989) Science 246, 1135-1142.
Puglisi JD (1995) Science 270,1200-1203
Gait & Karn (1993) Trends in Biochem. Sci. 18, 255-259
Weeks & Crothers (1991) Cell 66, 577-588