Readings for Advanced Molecular Biology, Fall
2008
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Cell Structure, Sept. 4, Chap. 1
Inside
a Living Cell, Goodsell, D., Trends in Biological Sciences 16, 203-206
(1991).
The
Depletion
Attraction: An Underappreciated Force Driving Cellular
Organization, D. Marenduzzo, K. Finan, P. Cook, J. Cell Biol. 175,
681-686 (2006).
Nucleic Acid Structure, Sept. 9, Chap. 2
Helical
Repeat of DNA in Solution, J. Wang, Proc. Natl. Acad. Sci. USA 76,
200-203
(1979).
DNA
Flexibility Studied by Covalent Closure of Short Fragments into
Circles, D.
Shore, J. Langoushi, R. Baldwin, Proc. Natl. Acad. Sci. USA 78,
4833-4837
(1981).
Electrophoretic
Separations of Large DNA Molecules by Periodic Inversion of the
Electric Field,
C. Carle, M. Frank, M. Olson, Science 232, 65-68 (1986).
DNA Synthesis, Sept. 11, Chap. 3
The
Localization of Replication Origins on ARS Plasmids in S. cerevisiae,
B.
Brewer, W. Fangman, Cell 51, 463-471 (1987).
E.
coli oriC and the dnaAGene
Promoters are Sequestered from dam Methyltransferase Following the
Passage of
the Chromosomal Replication Fork, Campbell, J., Kleckner, N., Cell 62,
967-979
(1990).
RNA Synthesis, Sept. 16, 18, Chap. 4
Transcription
Against an Applied Force, H. Yin, M. Wang, K. Svoboda, R. Landick, S.
Block, J.
Gelles, Science 270, 1653-1657 (1995).
Promoter
unwinding and promoter clearance by RNA polymerase: Detection by
single-molecule DNA nanomanipulation Andrey Revyakin, Richard H.
Ebright, and
Terence R. Strick, Proc. Nat. Acad. Sci. USA 101, 4778-80 (2004).
Association
of RNA Polymerase with Transcribed Regions in Escherichia
coli, J. Wade, K. Struhl, Proc.
Natl. Acad. Sci. USA 101, 17777- 82
(2004).
Noncoding RNAs, RNAi, and RNA Processing, Sept. 23, Chap. 5
A
Compensatory Base Change in U1 snRNA Suppresses a 5' Splice Site
Mutation, Y.
Zhuang, A. Weiner, Cell 46, 827-835 (1986).
Potent
and Specific Genetic Interference by Double-stranded RNA in
Caenorhabditis
elegans, A. Fire, S. Xu, M. Montgomery, S. Kostas, S. Driver, C. Mello,
Nature
391, 806-811 (1998).
DsrA
RNA Regulates Translation of RpoS Message by an Anti-antisense
Mechanism,
Independent of its Action as an Antisilencer of Transcription, N.
Majdalani, C.
Cunning, D. Sledjeski, T. Elliott, S. Gottesman, Proc. Natl. Acad. Sci.
USA 95,
12462-12467 (1998).
Eukaryotic Nucleus, Sept. 25
Crystal
Structure of the Nucleosome Core Particle at 2.8 Angstrom Resolution,
K. Luger,
A. Mader, R. Richmond, D. Sargent, T. Richmond, Nature 389, 251-260
(1997).
Rapid
Spontaneous Accessibility of Nucleosomal DNA, G. Li, C. Bustamante, J.
Widom,
Nat. Struct. and Mol. Biol. 12, 46-52 (2005).
Protein Structure, Sept. 30, Chap. 6
Protein
Structure by Mechanical Triangulation, H. Dietz, M. Rief,
Proc.
Natl. Acad. Sci. USA 103, 1244-47 (2006).
Xray
Structure of the GCN4 Leucine Zipper, a Two-stranded, Parallel Coiled
Coil, E.
O'Shea, J. Klemm, P. Kim, T. Alber, Science 254, 539-544 (1991).
Design
of a Novel Globular Protein Fold with Atomic-level
Accuracy, Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker
D, Science 21, 1364-8 (2003).
Protein Synthesis, Ribosome Function Oct. 2, Chap. 7
The
Transfer RNA Identity Problem: A Search for Rules, M. Saks, J. Sampson,
J.
Abelson, Science 263, 191-197 (1994).
The
structural basis of ribosome activity in peptide bond synthesis, P.
Nissen, J.
Hansen, N. Ban, P. Moore, T. Steitz, Science 289, 920-930 (2000).
Role
of a Peptide Tagging System in Degradation of Proteins Synthesized from
Damaged Messenger RNA, K. Keiler, P. Waller, R. Sauer, Science 271,
990-993, (1996).
Genetics, Oct. 9, Chap. 8
The
Processing of Recombination Intermediates: Mechanistic Insights from
Studies of
Bacterial Proteins, S. West, Cell 76, 915 (1994)
General
Model for Genetic Recombination, M. Meselson, C. Radding, Proc. Natl.
Acad.
Sci. USA 72, 358-361 (1975).
Genetic Engineering, Oct. 14, 16, 21, Chaps. 9, 10
The
Two-hybrid System: A Method to Identify and Clone Genes for Proteins
that Interact
with a Protein of Interest, C. Chien, P. Bartel, R. Sternglanz, S.
Fields,
Proc. Natl. Acad. Sci. USA 88, 9578-9582 (1991).
An
RNA Motif that Binds ATP, M. Sassanfar, J. Szostak, Nature 364, 550-553
(1993).
Regional
Codon Randomization: Defining a TATABinding Protein Surface Required
for RNA
Polymerase III Transcriiption, B. Cormack, K. Struhl, Science 262,
244-248
(1993).
PCR
Analysis of Tissue Samples from the 1979 Sverdlovsk Anthrax Victims:
The
Presence of Multiple Bacillus Anthrax Strains in Different Victims, P.
Jackson,
M. Hugh-Jones, D. Adair, G. Green, K. Hill, C. Kuske, L. Grinberg, F.
Abromova,
P. Keim, Proc. Natl. Acad. Sci. USA 95, 1224-1229 (1998).
Protein
Design by Binary Patterning of Polar and Nonpolar Amino Acids, S.
Kamtkar, J.
Schiffer, H. Xiong, J. Babik, M. Hecht, Science 262, 1680-1685 (1993).
Molecular
Computation of Solutions to Combinatorial Problems, L. Adleman, Science
266, 1021-24 (1994).
Identification
of D-peptide Ligands Through Mirrorimage Phage Display, T. Schumacher.
L. Mayr,
D. Minor, Jr., M. Milhollen, M. Burgess, P. Kim, Science 271, 1854-1857
(1996).
Multiple
Ebola Virus Transmission Events and Rapid Decline of Cental African
Wildlife,
E. Leroy, P. Rouquet, P. Formenty, S. Souquiere, A. Kilbourne, J.
Froment, M.
Bermejo, S. Smit, W. Karesh, R. Swanepoel, S. Zake, Science 303, 387-90
(2004).
Probing TBP Interactions in
Transcription Initiation and Reinitiation with RNA Aptamers that Act in
Distinct Modes, X. Fan, H. Shi, K. Adelman, J. Lis, PNAS 101, 6934-39
(2004).
Genomics and Proteomics, Oct. 23
Global
Identification of Human Transcribed Sequences with Genome
Tiling
Arrays, Bertone, et. al. Science 306, 2242-46, 2004.
An
in Vivo Map of the yeast Protein Interactome, K. Tarassov et. al.,
Science 320, 1465-1470 (2008).
Independence
of Replicsomes in Escherichia coli Chromosomal
Replication,
A. Breier, H. Weier, N. Cozzarelli, Proc. Natl. Acad. Sci. USA 102,
3942-47
(2005).
The
Development and Application of Methods for Activity-based
Protein Profiling, N. Jessani,B. Cravatt, Current Opinion in Chemical
Biology 8, 54-59 (2004)
Bioinformatics, Oct. 28
A
General Method Applicable to the Search for Similarities in the Anino
Acid
Sequence of two Proteins, S. Needleman, C. Wunsch, J. Mol. Biol. 48,
443-53
(1970).
http://www.ncbi.nih.gov/Education/BLASTinfo/similarity.html.
Lactose Operon, Oct 30, Chap. 11
Identification
of the Functional Subunit of a Dimeric Transcription Activator Protein
by Use
of Oriented Heterodimers, Y. Zhou, S. Busby, R. Ebright, Cell 73,
375-379
(1993).
Mechanism
of Corepressor-mediated Specific DNA Binding by the Purine Repressor,
M.
Schumacher, K. Choi, F. Lu, H. Zalkin, R. Brennan,Cell 83, 147-155
(1995).
Modeling
the Lac Repressor-Operator Assembly:
The Influence of DNA Looping on Lac Repressor Conformation, D.
Swigon, B. Coleman, W. Olson, Proc. Natl. Acad. Sci. USA 103, 9879-84
(2006).
Arabinose Operon, Nov. 4, Chap. 12
DNA
Looping and Unlooping by AraC Protein, R. Lobell, R. Schleif, Science
250,
528-532 (1990).
Regulation
of the L-arabinose Operon of Escherichia coli, R. Schleif, Trends in
Genetics
16, 559-565 (2000).
The
Role of Rigidity in DNA Looping-unlooping by AraC, T. Harmer, M. Wu, R.
Schleif, Proc. Natl. Acad. Sci. USA 98, 427-431 (2001).
Arm-Domain
Interactions in AraC, B. Saviola, R. Seabold, R. Schleif, J. Mol. Biol.
278,
539-548 (1998).
Prions and the Tryptophan Operon, Nov. 6, Chap. 13
Mice
Devoid of PrP are Resistant to Scrapie, H. Bueler, A. Aguzzi, A.
Sailer, R.
Greiner, P. Autenried, M. Aguet, C. Weissmann, Cell 73, 1339-1347
(1993).
[URE3]
as an Altered URE2 Protein: Evidence for a Prion Analog in Saccharomyces
cerevisiae, R. Wickner, Science 264, 566-569 (1994).
Yeast Mating Type, Nov. 13, Chap. 16
A
700 bp cis-Acting Region Controls Mating-Type Dependent Recombination
Along the
Entire Left Arm of Yeast Chromosome III. X. Wu, J. Haber, Cell 87,
277-285
(1996).
“Mutagenesis”
by Peptide Aptamers Identifies Genetic Network Members and Pathway
Connections,
C. Geyer, A. Colman-Lerner, R. Brent, Proc. Natl. Acad. Sci. USA 96,
8567-72
(1999).
Molecular Aspects of Development, Nov. 18, Chap. 17
P-ElementMediated
Enchancer Detection: An Efficient Method for Isolating and
Characterizing
Developmentally Regulated Genes in Drosophila, Wilson, C., Pearson, R.,
Bellen,
H., O'Kane, C., Grossniklaus, U., and Gehring, W., Genes and
Development 3,
1288-1300 (1989).
Induction
of Ectopic Eyes by Targeted Expression of the Eyeless Gene in
Drosophila, G.
Halder, P. Callaerts, W. Gehring, Science 267, 1788-1792 (1995).
Determination
of Left-right Patterning of the Mouse Embryo by Artificial Nodal Flow,
S.
Nonaka, H. Shiratori, Y. Saljoh, H. Hamada, Nature 418, 96-99 (2002).
Transposable Elements, Nov. 20, Chap. 19
Genetic
Evidence that Tn10 Transposes by a Nonreplicative Mechanism, J. Bender,
N.
Kleckner, Cell 45, 801-815 (1986).
Role
of DNA Topology in Mu Transposition: Mechanism of Sensing the Relative
Orientation of Two DNA Segments, Craigie, R., Mizuuchi, K., Cell 45,
793-800
(1986).
Molecular Aspects of the Immune System, Nov. 25, Chap. 20
Mismatch
Repair Co-opted by Hypermutation, M. Cascalho, J. Wong, C. Steinberg,
M. Wabl,
Science 279, 1207-1210 (1998).
Cell-free
V(D)J Recombination, D. Ramsden, T. Paull, M. Gellert, Nature 388,
488-491
(1997).
Activation-induced
cytidine deaminase turns on somatic hypermutation in hybridomas, M.
Bardwell, C.
Woo, M. Fan, M. Shulman, M. Scharff, Nature, 415, 802-802 (2002).
Oncogenesis, Dec. 2, Chap. 23
Dietary
Carcinogens and Anticarcinogens, B. Ames, Science 221, 1256-1264 (1983).
An
Adenovirus Mutant that Replicates Selectively in p53-deficient Human
Tumor
Cells, J. Bischoff, D. Kirn, A. Williams, C. Heise, S. Horn, M. Muna,
L. Ng, J.
Nye, A. Sampson-Johannes, A. Fattaey, F. McCormick, Science 274,
373-376
(1996).
Enzyme
Activity Profiles of the Secreted and Membrane
Proteome that Depict Cancer Cell Invasiveness, N. Jessani, Y. Liu, M.
Humphrey, B. Cravatt
Proc. Natl. Acad. Sci. USA 99, 10335–10340 (2002).