Extended References

Structure of Nucleic Acids

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Cech, T. R. 2009. Evolution of biological catalysis: ribozyme to RNP enzyme. Cold Spring Harbor Symp. Quant. Biol. 74:11–16.

Dickerson, R. E. 1992. DNA structure from A to Z. Meth. Enzymol. 211:67–111.

Kornberg, A., and T. A. Baker. 2005. DNA Replication. University Science, chap. 1.

Lilley, D. M. 2005. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struc. Biol. 15:313–323.

Vicens, Q., and T. R. Cech. 2005. Atomic level architecture of group I introns revealed. Trends Biochem. Sci. 31:41–51.

Wang, J. C. 1980. Superhelical DNA. Trends Biochem. Sci. 5:219–221.

Wigley, D. B. 1995. Structure and mechanism of DNA topoisomerases. Ann. Rev. Biophys. Biomol. Struc. 24:185–208.

Transcription of Protein-Coding Genes and Formation of Functional mRNA

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The Decoding of mRNA by tRNAs

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Stepwise Synthesis of Proteins on Ribosomes

Ban N., et al. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289:905–920.

Belousoff, M. J., et al. 2010. Ancient machinery embedded in the contemporary ribosome. Biochem. Soc. Trans. 38:422–427.

Frank, J., and R. L. Gonzalez, Jr. 2010. Structure and dynamics of a processive Brownian motor: the translating ribosome. Ann. Rev. Biochem. 79:381–412.

Jackson, R.J., et al. 2010. The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Rev. Mol. Cell Biol. 11:113–127.

Korostelev, A., D. N. Ermolenko, and H. F. Noller. 2008. Structural dynamics of the ribosome. Curr. Opin. Chem. Biol. 12:674–683.

Livingstone, M., et al. 2010. Mechanisms governing the control of mRNA translation. Phys. Biol. 7(2):021001.

Sarnow, P., R. C. Cevallos, and E. Jan. 2005. Takeover of host ribosomes by divergent IRES elements. Biochem. Soc. Trans. 33:1479–1482.

Steitz, T. A. 2008. A structural understanding of the dynamic ribosome machine. Nature Rev. Mol. Cell Biol. 9:242–253.

Wimberly, B. T., et al. 2000. Structure of the 30S ribosomal subunit. Nature 407:327–339.

Yusupova, G. and M. Yusupov. 2014. High-resolution structure of the eukaryotic 80S ribosome. Ann. Rev. Biochem. 83:467–486. http://www.annualreviews.org/doi/suppl/10.1146/annurev-biochem-060713-035445.

DNA Replication

DePamphilis, M. L., ed. 2006. DNA Replication and Human Disease. Cold Spring Harbor Laboratory Press.

Gai, D., Y. P. Chang, and X. S. Chen. 2010. Origin DNA melting and unwinding in DNA replication. Curr. Opin. Struc. Biol. 20(6):756–762.

Kornberg, A., and T. A. Baker. 2005. DNA Replication. University Science.

Langston, L. D., C. Indiani, and M. O’Donnell. 2009. Whither the replisome: emerging perspectives on the dynamic nature of the DNA replication machinery. Cell Cycle 8:2686–2691.

Langston, L. D., and M. O’Donnell. 2006. DNA replication: keep moving and don’t mind the gap. Mol. Cells 23:155–160.

Schoeffler, A. J., and J. M. Berger. 2008. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Quart. Rev. Biophys. 41:41–101.

Stillman, B. 2008. DNA polymerases at the replication fork in eukaryotes. Cell 30:259–260.

DNA Repair and Recombination

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Barnes, D. E., and T. Lindahl. 2004. Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Ann. Rev. Genet. 38:445–476.

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Friedberg, E. C., et al. 2006. DNA repair: from molecular mechanism to human disease. DNA Repair 5:986–996.

Haber, J. E. 2000. Partners and pathways repairing a double-strand break. Trends Genet. 16:259–264.

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Khuu, P. A., et al. 2006. The stacked-X DNA Holliday junction and protein recognition. J. Mol. Recog. 19:234–242.

Lilley, D. M., and R. M. Clegg. 1993. The structure of the four-way junction in DNA. Ann. Rev. Biophys. Biomol. Struc. 22:299–328.

Mirchandani, K. D., and A. D. D’Andrea. 2006. The Fanconi anemia/BRCA pathway: a coordinator of cross-link repair. Exp. Cell Res. 312:2647–2653.

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Viruses: Parasites of the Cellular Genetic System

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Hull, R. 2002. Mathews’ Plant Virology. Academic Press.

Klug, A. 1999. The tobacco mosaic virus particle: structure and assembly. Phil. Trans. R. Soc. Lond. B Biol. Sci. 354:531–535.

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Kornberg, A., and T. A. Baker. 1992. DNA Replication, 2d ed. W. H. Freeman and Company. Good summary of bacteriophage molecular biology.