Chemistry/Biological and Bioanalytical Chemistry

"The Role of Ligand Density and Size in Mediating Quantum Dot Nuclear Transport." P. Tang, S. Sathiamoorthy, L. Lustig, R. Ponzielli, I. Inamoto, L. Z. Penn, J. A. Shin, & W.C.W. Chan, Small, 2014, 10, 4182-4192. doi: 10.1002/smll.201401056. "Boundaries of the Origin of Replication: Creation of a pET-28a-Derived Vector with p15A Copy Control Allowing Compatible Coexistence with pET Vectors." S. Sathiamoorthy & J. A. Shin, PLoS ONE, 2012, 7, e47259. doi:10.1371/journal.pone.0047259. "The bZIP Dimer Localizes at DNA Full-Sites Where Each Basic Region Can Alternately Translocate and Bind to Subsites at the Half-Site." I. Chan, T. Al-Sarraj, H. S. Shahravan, A. V. Fedorova, & J. A. Shin, Biochemistry, 2012, 51, 6632-6643. "Forced homodimerization of the Fos leucine zipper in designed bHLHZ-like hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos." G. Chen, A. T. De Jong, & J. A. Shin, Molecular BioSystems, 2012, 8, 1286-1296. "Crystal structure of the minimalist Max-E47 protein chimera." F. Ahmadpour, R. Ghirlando, A. T. De Jong, J. A. Shin, & A. Guarne, PLoS ONE, 2012, 7, e32136 (doi:10.1371/journal.pone.0032136). "FRep: a fluorescent protein-based bioprobe for in vivo detection of protein:DNA interactions." S. H. Shahravan, I. T. Li, K. Truong, & J. A. Shin, Analytical Chemistry, 2011, 83, 9643-9650. "Reengineering natural design by rational design and in vivo library selection: the HLH domain in bHLHZ proteins is a unique requirement for DNA-binding function." J. Xu, H.-K. Chow, G. Chen, C. O. Damaso, A. Schwartz Mittelman, & J. A. Shin, Protein Engineering, Design, & Selection, 2010, 23, 337-346. "Max-E47, a designed minimalist protein that targets the E-box DNA site in vivo and in vitro." J. Xu, G. Chen, A. T. De Jong, S. H. Shahravan, & J. A. Shin. Journal of the American Chemical Society, 2009, 131, 7839-7848. "Hybrids of the bHLH and bZIP Protein Motifs Display Different DNA-Binding Activities in vivo vs. in vitro." H.-K. Chow, J. Xu, S. H. Shahravan, A. T. De Jong, G. Chen, & J. A. Shin. PLoS ONE, 2008, 3, e3514. doi:10.1371/journal.pone.0003514. "AhR/Arnt:XRE interaction: turning false negatives into true positives in the modified yeast one-hybrid assay." G. Chen & J. A. Shin. Analytical Biochemistry, 2008, 382, 101-106. "Design of a single plasmid-based modified yeast one-hybrid system for investigation of in vivo protein-protein and protein-DNA interactions." G. Chen, L. M. DenBoer, & J. A. Shin. BioTechniques, 2008, 45, 295-304. "The bZIP targets overlapping DNA sub-sites within a half site resulting in increased binding affinities." I. Chan, S. H. Shahravan, A. V. Fedorova, & J. A. Shin. Biochemistry, 2008, 47, 9646-9652. "Enhancing the specificity of the enterokinase cleavage reaction to promote efficient cleavage of a fusion tag." S. H. Shahravan, X. Qu, I. Chan, & J. A. Shin. Protein Expression and Purification, 2008, 59, 314-319. "The GCN4 bZIP Targets Noncognate Gene Regulatory Sequences: Quantitative Investigation of Binding at Full and Half Sites." I. Chan, A. V. Fedorova, & J. A. Shin. Biochemistry, 2007, 46, 1663-1671. "The GCN4 bZIP Can Bind to Noncognate Gene Regulatory Sequences." A. V. Fedorova, I. Chan, & J. A. Shin. Biochimica et Biophysica Acta (Proteins and Proteomics), 2006, 1764, 1252-1259. "Minimalist Proteins: Design of New Molecular Recognition Scaffolds." J. A. Shin. Pure and Applied Chemistry, 2004, 76, 1579-1590. "Sequence-Specific Recognition of DNA by Hydrophobic, Alanine-scanning Mutants of the bZIP Motif Investigated by Fluorescence Anisotropy." G. H. Bird, A. R. Lajmi, & J. A. Shin. Biopolymers, 2002, 65, 10-20. "MALDI-TOF Mass Spectrometry Characterization of Hydrophobic Basic Region/Leucine Zipper Proteins." G. H. Bird & J. A. Shin. Biochimica et Biophysica Acta (Protein Structure & Molecular Enzymology), 2002, 1597, 252-259. "Manipulation of Temperature to Improve Solubility of Hydrophobic Proteins and Cocrystallization with Matrix for Analysis by MALDI-TOF Mass Spectrometry." G. H. Bird, A. R. Lajmi, & J. A. Shin. Analytical Chemistry, 2002, 74, 219-225. "The Contribution of the Methyl Groups on Thymine Bases to Binding Specificity and Affinity by Alanine-rich Mutants of the bZIP Motif." K. J. Kise Jr. & J. A. Shin. Bioorganic and Medicinal Chemistry, 2001, 9, 2485-2491. "Short, Hydrophobic, Alanine-based Proteins Based on the bZIP Motif: Overcoming Inclusion Body Formation and Protein Aggregation During Overexpression, Purification, and Renaturation." A. R. Lajmi, T. R. Wallace, & J. A. Shin. Protein Expression and Purification, 2000, 18, 394-403. "Minimalist, Alanine-based, Helical Protein Dimers Bind to Specific DNA Sites." A. R. Lajmi, M. E. Lovrencic, T. R. Wallace, R. R. Thomlinson, & J. A. Shin. Journal of the American Chemical Society, 2000, 122, 5638-5639. “Specific DNA Binding Peptide-Derivatized Solid Support.” J. A. Shin. Bioorganic and Medicinal Chemistry Letters, 1997, 7, 2367-2372. "Mechanistic Studies of an Antibody with Chorismate Mutase Activity." J. A. Shin & D. Hilvert. Bioorganic and Medicinal Chemistry Letters, 1994, 4, 2945-2948. "Orientation of the Lac Repressor DNA Binding Domain In Complex with the Left Lac Operator Half Site Characterized by Affinity Cleaving." J. A. Shin, R. H. Ebright, & P. B. Dervan. Nucleic Acids Research, 1991, 19, 5233-5236. "Cooperative Binding of Oligonucleotides to DNA by Triple Helix Formation: Dimerization via Watson-Crick Hydrogen Bonds." M. D. Distefano, J. A. Shin, & P. B. Dervan. Journal of the American Chemical Society, 1991, 113, 5901-5902.

"Orientation of the Putative Recognition Helix in the DNA-Binding Domain of Hin Recombinase Complexed with the Hix Site." D. P. Mack, J. P. Sluka, J. A. Shin, J. H. Griffin, M. I. Simon, & P. B. Dervan. Biochemistry, 1990, 29, 6561-6567.