Note this list is based on last years course and I will be updating as we go through topics




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Reference List 5469

C:\web-rbw\5469-2010


NOTE This list is based on last years course and I will be updating as we go through topics.


Temple University has free electronic access to most of these references. Currently my bibliography software does not print out all the links to these articles or the journal sites. Ask the librarian (Thomas Heverin will be covering Biology and Chemistry. 1-4725; thomas.heverin@temple.edu) for some hints on accessing them. I keep a folder on my browser in which I store links to the home or archive pages of journals I use. Some journals require that you log on through a temple computer or at least begin your search through the Temple library homepage so that the IPS address is recognized as coming from a subscriber to the journal.


One or two references are too old to be available on-line.


Required References

Mirkin,S.M. (2007). Expandable DNA repeats and human disease. Nature 447, 932-940.
Abstract: Nearly 30 hereditary disorders in humans result from an increase in the number of copies of simple repeats in genomic DNA. These DNA repeats seem to be predisposed to such expansion because they have unusual structural features, which disrupt the cellular replication, repair and recombination machineries. The presence of expanded DNA repeats alters gene expression in human cells, leading to disease. Surprisingly, many of these debilitating diseases are caused by repeat expansions in the non-coding regions of their resident genes. It is becoming clear that the peculiar structures of repeat-containing transcripts are at the heart of the pathogenesis of these diseases

http://www.nature.com/nature/journal/v447/n7147/full/nature05977.html


If you do no not have access to a textbook which gives an overview of chromatin and chromatin regulation you should read as a foundation for class material:

Felsenfeld,G. and Groudine,M. (2003). Controlling the double helix. Nature 421, 448-453.
Abstract: Chromatin is the complex of DNA and proteins in which the genetic material is packaged inside the cells of organisms with nuclei. Chromatin structure is dynamic and exerts profound control over gene expression and other fundamental cellular processes. Changes in its structure can be inherited by the next generation, independent of the DNA sequence itself. http://www.nature.com/nature/journal/v421/n6921/full/nature01411.html

Recommended References. Suggestion: –


Look up the reference on-line. Get the News and Views article too (See end of this ref.)

A lot of structural detail so take note of some of the key procedures, experiments and conclusions .


Luger,K., Mader,A.W., Richmond,R.K., Sargent,D.F., and Richmond,T.J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution [see comments]. Nature 389, 251-260.
Abstract: The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.
Notes: http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v389/n6648/full/389251a0_fs.html
News & Views Comments in Nature. 1997 Sep 18;389(6648):251-60 at http://www.nature.com/doifinder/10.1038/38386

Woychik,N.A. and Hampsey,M. (2002). The RNA polymerase II machinery: structure illuminates function. Cell 108, 453-463. A good overview but there are more up to date review articles in the background reference section. Abstract: Essential components of the eukaryotic transcription apparatus include RNA polymerase II, a common set of initiation factors, and a Mediator complex that transmits regulatory information to the enzyme. Insights into mechanisms of transcription have been gained by three-dimensional structures for many of these factors and their complexes, especially for yeast RNA polymerase II at atomic resolution.


Background References. Suggestion: –


Read the abstracts.

If one interests you, look up the reference on-line

Skim through it first – often you may find one section, especially early on or a figure helpful.

do not feel obligated to print out every reference - that is not the purpose of this list!


Molecular Interactions and Weak Bonds

Elf,J., Li,G.W., and Xie,X.S. (2007). Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191-1194.
Abstract: Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characterized the nonspecific binding to DNA, one-dimensional (1D) diffusion along DNA segments, and 3D translocation among segments through cytoplasm at the single-molecule level. In searching for the operator, a lac repressor spends approximately 90% of time nonspecifically bound to and diffusing along DNA with a residence time of <5 milliseconds. The methods and findings can be generalized to other nucleic acid binding proteins.

http://www.sciencemag.org/cgi/content/full/316/5828/1191


Viadiu,H. and Aggarwal,A.K. (2000). Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol Cell 5, 889-895.
Abstract: The central problem faced by DNA binding proteins is how to select the correct DNA sequence from the sea of nonspecific sequences in a cell. The problem is particularly acute for bacterial restriction enzymes because cleavage at an incorrect DNA site could be lethal. To understand the basis of this selectivity, we report here the crystal structure of endonuclease BamHI bound to noncognate DNA. We show that, despite only a single base pair change in the recognition sequence, the enzyme adopts an open configuration that is on the pathway between free and specifically bound forms of the enzyme. Surprisingly, the DNA drops out of the binding cleft with a total loss of base-specific and backbone contacts. Taken together, the structure provides a remarkable snapshot of an enzyme poised for linear diffusion (rather than cleavage) along the DNA
Notes: http://www.molecule.org/content/article/abstract?uid=PIIS1097276500803299


Fersht,A.R. (1987). The hydrogen bond in molecular recognition. Trends Biochem Sci. 12, 301-304.
Abstract: The hydrogen bond is a ubiquitous element of molecular recognition. Recent experiments on engineered enzymes, modified inhibitors and synthetic DNA duplexes indicate that an individual uncharged hydrogen bond contributes some 0.5 to 1.8 kcal mol-1 to binding energy and a factor of two to twenty to specificity. Unfavorable steric interactions or unpaired charged donors or acceptors can provide far higher specificity.

The article may be found at this link and then scrolling to page 301.

http://www.sciencedirect.com/science?_ob=PublicationURL&_method=list&_tockey=%23toc%235180%231987%23999879999%23371049%23FLP%23&_auth=y&_version=1&refSource=toc&_pubType=J&_cdi=5180&md5=29b4a1e2bd093f8164a061debf31126a&chunk=0&view=c&go=next&count=241&count=241&NEXT_LIST=Y

Verkman,A.S. (2002). Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem Sci. 27, 27-33.
Abstract: Diffusion of solutes and macromolecules in aqueous cellular compartments is required for numerous cellular processes including metabolism, second messenger signaling and protein-protein interactions. The view of the cell interior has evolved from that of a viscous gel to that of a watery but crowded compartment. Recent measurements of fluorescent probe diffusion using photobleaching, correlation microscopy and time-resolved anisotropy methods, have indicated unexpectedly high mobilities of small solutes and macromolecules. This review evaluates experimental evidence defining the rates and barriers for molecular diffusion in cells. Possible implications of regulated molecular diffusion as a rate-limiting step in cell metabolism, and with respect to the delivery of therapeutic agents, are discussed

Nucleic Acids

Mirkin,S.M. (2007). Expandable DNA repeats and human disease. Nature 447, 932-940.
Abstract: Nearly 30 hereditary disorders in humans result from an increase in the number of copies of simple repeats in genomic DNA. These DNA repeats seem to be predisposed to such expansion because they have unusual structural features, which disrupt the cellular replication, repair and recombination machineries. The presence of expanded DNA repeats alters gene expression in human cells, leading to disease. Surprisingly, many of these debilitating diseases are caused by repeat expansions in the non-coding regions of their resident genes. It is becoming clear that the peculiar structures of repeat-containing transcripts are at the heart of the pathogenesis of these diseases

http://www.nature.com/nature/journal/v447/n7147/abs/nature05977.html;jsessionid=4A1C7D10134E91DCD83A8B51F18D4970


Ha,S.C., Lowenhaupt,K., Rich,A., Kim,Y.G., and Kim,K.K. (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437, 1183-1186.
Abstract: Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification
Notes: http://www.nature.com/nature/journal/v437/n7062/pdf/nature04088.pdf Comment in: Nature. 2005 Oct 20;437(7062):1097-8.

Leontis,N.B., Stombaugh,J., and Westhof,E. (2002). The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30, 3497-3531.
Abstract: RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs
Notes: http://nar.oupjournals.org/cgi/content/full/30/16/3497

Vinograd,J., Lebowitz,J., Radloff,R., Watson,R., and Laipis,P. (1965). The twisted circular form of polyoma viral DNA. Proc. Natl. Acad. Sci. U. S. A 53, 1104-1111.
Abstract: None available
Notes: http://www.jstor.org/view/00278424/ap000600/00a00400/0 ALTERNATIVELY http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=4287964

Keck,J.L. and Berger,J.M. (1999). Enzymes that push DNA around. Nat Struct. Biol 6, 900-902.
Abstract: DNA topoisomerases are proteins that regulate DNA topology in cells through selective cycles of DNA cleavage, manipulation, and religation. Two papers describe an ensemble of different protein conformations and nucleotide-protein complexes of Escherichia coli topoisomerase. These results lead to new insights about how this enzyme recognizes DNA and catalyzes supercoil relaxation.

http://www.nature.com/nsmb/journal/v6/n10/full/nsb1099_900.html


Genomes

Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J., Chen,Z., Dewell,S.B., Du,L., Fierro,J.M., Gomes,X.V., Godwin,B.C., He,W., Helgesen,S., Ho,C.H., Irzyk,G.P., Jando,S.C., Alenquer,M.L., Jarvie,T.P., Jirage,K.B., Kim,J.B., Knight,J.R., Lanza,J.R., Leamon,J.H., Lefkowitz,S.M., Lei,M., Li,J., Lohman,K.L., Lu,H., Makhijani,V.B., McDade,K.E., McKenna,M.P., Myers,E.W., Nickerson,E., Nobile,J.R., Plant,R., Puc,B.P., Ronan,M.T., Roth,G.T., Sarkis,G.J., Simons,J.F., Simpson,J.W., Srinivasan,M., Tartaro,K.R., Tomasz,A., Vogt,K.A., Volkmer,G.A., Wang,S.H., Wang,Y., Weiner,M.P., Yu,P., Begley,R.F., and Rothberg,J.M. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.
Abstract: The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.
Notes: http://www.nature.com/nature/journal/v437/n7057/pdf/nature03959.pdf Includes enormous amount of supplemental material. See News & Views Nature. 2005 Sep 15;437(7057):326-7.
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