Faculty Research Page

Stuart Linn

Stuart Linn

Professor Emeritus of Biochemistry, Biophysics and Structural Biology*
*And Member, Graduate Groups in Biophysics and Comparative Biochemistry

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Research Interests

Enzymes and DNA binding proteins involved in DNA damage responses, DNA repair and replication in mammalian cells. Dosimetry and signaling for the DNA damage response.  DNA polymerases.  Generation of DNA damage by reactive oxygen species (ROS).

Current Projects

DNA damage and repair. I am interested in proteins from human cells that recognize DNA damage then directly or indirectly mediate the DNA damage response: DNA repair, transcription response, cell cycle arrest, or apoptosis.

DNA polymerases. I am interested in the properties of DNA polymerase of human cells, particularly changes which occur with these enzymes in various cell states and with various accessory factors. I am also interested in the roles of individual human DNA polymerases in  DNA replicative and repair synthesis.

Reactive oxygen species:  I am interested in the generation of reactive oxygen species that damage DNA and the damages that they produce.

Selected Publications

 Linn, S.  (2015) Radicals in Berkeley?  J. Biol. Chem.: Reflections 290, 8748-8757.  (Published online 25  Feb. 2015: doi:10.1074/jbc.X115.644989)

Chattopadhyaya, R.  (2014) Oxidative damage to DNA constituents by iron-mediated Fenton reactions: the thymidine family.  J. Biomolec. Str. and Dynamics 32, 155-169.   (Published online 20 Dec. 2012:  doi10.1080/07391102.2012.745167)

Chattopadhyaya, R. and Goswami, B.  (2012) Oxidative damage to DNA constituents by iron-mediated Fenton reactions: the deoxyadenosine family.  J. Biomolec. Str. and Dynamics 30, 394-406.

Linn, S. (2012)  Life in the Serendipitous Lane: Excitement and Gratofocatopm om Studying DNA Repair.  DNA Repair 11, 595-605.

Linn, S. (2009)  Strategies and Considerations for Protein Purification.  In:  Guide to Protein Purification, Second edition, a volume of Methods in Enzymology, 463, 9-19. 

Itoh, T., Iwashita, S., Cohen, M.B., Meyerholz,  D. K., and Linn,  S.  (2007) DDB2 is a haplo-insufficient tumor suppressor and controls spontaneous germ cell apoptosis.  Human Molecular Genetics 16, 1578-1586.

Itoh, T. and Linn S.  (2007) The functions of mammalian DDB2 (XP-E) DNA Repair 6 (abstract).

 Itoh, T. and Linn, S. (2005).  The fate of p21CDKNIA in cells surviving UV-irradiation.  DNA Repair 4, 1457-1462.

Rai, P., Wemmer, D. E. and Linn, S. (2005) Preferential binding and structural distortion by Fe2+ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences. Nuc. Acids Res. 33, 497-510.

Itoh, T., Cado, D., Kamide, R., and Linn, S. (2004) DDB2 gene disruption leads to skin tumors and resistance to apoptosis after exposure to ultraviolet light but not a chemical carcinogen. Proc. Nat'l. Acad. Sci. USA 101, 2052-2057.

Sancar, A., Lindsey-Boltz, L. A., Unsal-Kacmaz, K. and Linn, S. M. (2004). Molecular Mechanisms of Mammalian DNA Repair and the DNA Damage Checkpoints. Ann. Rev. Bioch. 73, 39-85.

Asahara, H., Li, Y., Fuss, J., Hanes, D. S. Vlatkovic, N., Boyd, M. T., and Linn, S. (2003). Stimulation of Human DNA Polymerase epsilon by MDM2. Nuc. Ac. Res. 31, 2451-2459.

Rai, P., Cole, T.D., Thompson, E., Millar, D., and Linn, S. (2003). Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex sequences. Nuc. Ac. Res. 31, 2323-2332.

Itoh, T., O'Shea, C. and Linn, S. (2003). Impaired Regulation of Tumor Suppressor p53 Caused by Mutations in the Xeroderma Pigmentosum DDB2 Gene: Mutual Regulatory Interactions between p48DDB2 and p53. Mol. Cell. Biol. 23, 7540-7553.

Brumaghim, J. L., Li, Y., Henle, E. and Linn, S. (2003). Effects of Hydrogen Peroxide upon Pyridine Nucleotide Metabolism in Escherichia coli: changes in Enzyme Levels and Pyridine Nucleotide Pools and Studies of the Oxidation of NAD(P)H by Fe(III). J. Biol. Chem. 278, 42495-42504.

Nichols, A. F., Itoh, T., Zolezzi, F., Hutsell, S., and Linn, S. (2003). Basal transcriptional activation of human damage-specific DNA binding genes DDB1 and DDB2 by sp1, E2F, N-MYC and NF1 elements. Nuc. Ac. Res. 31, 562-569.

Zolezzi, F., Fuss, J., Uzawa, S. and Linn, S. (2002). Characterization of a Schizosaccharomyces Pombe Strain Deleted for a Sequence Homologue of the Human Damaged DNA Binding 1 (DDB1) Gene. J. Biol. Chem. 277, 41183-41191.

Human DNA polymerase epsilon colocalizes with DNA replication late, but not early in S phase. [J. Fuss and S. Linn (2002) J. Biol. Chem. 277, 8658-8666]

Localization of Fe2+ at an RTGR Sequence within a DNA duplex explains preferential cleavage by Fe2+ and H202. [P. Rai, T. D. Cole, D. E. Wemmer and S. Linn (2001) J. Mol. Biol. 312, 1089-1101]

Abnormal Regulation of DDB2 Gene Expression in Xeroderma Pigmentosum Group E Strains. [T. Itoh, A. Nichols and S. Linn (2001) Oncogene 20, 7041-7050]

Proteolysis of the human DNA polymerase epsilon catalytic subunit by caspase-3 and calpain specifically during apoptosis. [W. Liu, and S. Linn (2000) Nuc. Ac. Res. 28, 4180-4188]

MDM2 interacts with the carboxy terminus of the catalytic subunit of DNA polymerase epsilon. [N. Vlatkovic, S. Guerrera, Y. Li, S. Linn, D. S. Haines, and M. T. Boyd (2000) Nuc. Ac. Res. 28, 3581-3586]

Identification and Cloning of Two Histone-fold Motif Containing Subunits of HeLa DNA Polymerase epsilon. [Y. Li, Z. F. Pursell, and S. Linn (2000) J. Biol. Chem. 275, 23247-23252]

Nuclear Transport of Human DDB Protein Induced by Ultraviolet Light. [W. Liu, A. F. Nichols, J. A. Graham, R. Dualan, A. Abbas, and S. Linn (2000) J. Biol. Chem. 275, 21429-21434]

Human Damage-specific DNA Binding Protein p48: Characterization of XPE Mutations and Regulation Following UV-irradiation. [A. F. Nichols, T. Itoh, J. A. Graham, W. Liu, M. Yamaizumi, and S. Linn (2000) J. Biol. Chem. 275, 21422-21428]

The Naturally Occurring Mutants of DDB are Impaired in Stimulating Nuclear Import of the p125 Subunit and E2F1-Activated Transcription. [P. Shiyanov, S. A. Hayes, M. Donepudi, A. F. Nichols, S. Linn, B. L. Slagle, and P. Raychaudhuri (1999) Mol.Cell. Biol. 19, 4935-4943]

Sequence-specific DNA Cleavage by Fe2+-mediated Fenton Reactions has Possible Biological Implications. [E. S. Henle, Z. Han, N. Tang, P. Rai, Y. Luo, S. and Linn (1999) J. Biol. Chem. 274, 962-971]

Formation, Prevention and Repair of DNA Damage by Iron/Hydrogen Peroxide. [E. S. Henle and S. Linn (1997) J. Biol. Chem. 272, 19095-19098]

Purification, cDNA cloning and Gene Mapping of the Small Subunit of Human DNA Polymerase e. [Y. Li, H. Asahara, V. Patel, S. Zhou, and S. Linn (1997) J. Biol. Chem. 272, 32337-32344]

Fe2+, Fe3+ and Oxygen React with DNA-Derived Radicals Formed During Iron-Mediated Fenton Reactions. [E. S. Henle, Y. Luo, and S. Linn (1996) Biochemistry 35, 12212-12219]


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Last Updated 2015-08-27