Publications

Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. (2011) Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleasesNucleic Acids Res. 39, 381-392. 

Ozen A, Haliloğlu T, Schiffer CA. (2011) Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate EnvelopeJ Mol Biol. 410, 726-744.

Filion TM, Xu J, Prasad ML, Song J. (2011) In vivo tissue responses to thermal-responsive shape memory polymer nanocomposites. Biomaterials. 32, 985-991. 

Romano KP, Laine JM, Deveau LM, Cao H, Massi F, Schiffer CA. (2011) Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A proteaseJ Virol. 85, 6106-6116.

Metelev V, Zhang S, Tabatadze D, Bogdanov A. (2011) Hairpin-like fluorescent probe for imaging of NF-κB transcription factor activity. Bioconjug Chem. 22, 759-765. 

Xu J, Prifti F, Song J. (2011) A Versatile Monomer for Preparing Well-Defined Functional Polycarbonates and Poly(ester-carbonates). Macromolecules. 44, 2660-2667.

Hua Z, Lvov A, Morin TJ, Kobertz WR. (2011) Chemical control of metabolically-engineered voltage-gated K(+) channels. Bioorg Med Chem Lett. Apr 28. [Epub ahead of print]

Christensen RG, Gupta A, Zuo Z, Schriefer LA, Wolfe SA, Stormo GD. (2011) A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificityNucleic Acids Res. 39, e83

Liu P, Smits J, Ayers DC, Song J. (2011) Surface mineralization of Ti6Al4V substrates with calcium apatites for the retention and local delivery of recombinant human bone morphogenetic protein-2. Acta Biomater. 7, 3488-3495. 

Rusha L, Miller SC. (2011) Design and application of esterase-labile sulfonate protecting groups. Chem Commun (Camb). 47, 2038-2040

Filion TM, Kutikov A, Song J. (2011) Chemically modified cellulose fibrous meshes for use as tissue engineering scaffoldsBioorg Med Chem Lett. Apr 14. [Epub ahead of print]

Shazeeb MS, Sotak CH, DeLeo M 3rd, Bogdanov A Jr. (2011) Targeted signal-amplifying enzymes enhance MRI of EGFR expression in an orthotopic model of human gliomaCancer Res. 71, 2230-2239. 

Filion TM, Li X, Mason-Savas A, Kreider JM, Goldstein SA, Ayers DC, Song J. (2011) Elastomeric osteoconductive synthetic scaffolds with acquired osteoinductivity expedite the repair of critical femoral defects in ratsTissue Eng Part A. 17, 503-511. 

Romano KP, Ali A, Royer WE, Schiffer CA. (2010) Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor bindingProc Natl Acad Sci USA. 107, 20986-20991. 

Reddy GR, Thompson WC, Miller SC. (2010) Robust light emission from cyclic alkylaminoluciferin substrates for firefly luciferaseJ Am Chem Soc. 132, 13586-13587.

Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Schiffer CA, Rana TM. (2010) Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinonesJ Med Chem. 53, 7699-7708.

Miller SC. (2010) Profiling sulfonate ester stability: identification of complementary protecting groups for sulfonatesJ Org Chem. 75, 4632-4635.

Straza MW, Paliwal S, Kovi RC, Rajeshkumar B, Trenh P, Parker D, Whalen GF, Lyle S, Schiffer CA, Grossman SR. (2010) Therapeutic targeting of C-terminal binding protein in human cancerCell Cycle. 9, 3740-3750. 

Xu J, Song J. (2010) High performance shape memory polymer networks based on rigid nanoparticle cores.Proc Natl Acad Sci USA107, 7652-7657.

Bandaranayake RM, Kolli M, King NM, Nalivaika EA, Heroux A, Kakizawa J, Sugiura W, Schiffer CA. (2010) The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathwaysJ Virol. 84, 9995-10003. 

Cai Y, Schiffer CA. (2010) Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRVJ Chem Theory Comput. 6, 1358-1368.

Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. (2010) Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistanceJ Virol. 84, 5368-5378. 

Shandilya SM, Nalam MN, Nalivaika EA, Gross PJ, Valesano JC, Shindo K, Li M, Munson M, Royer WE, Harjes E, Kono T, Matsuo H, Harris RS, Somasundaran M, Schiffer CA. (2010) Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfacesStructure18, 28-38.

Zhang S, Bogdanov A Jr. (2009) Plate Capture Assay of Fluorescent Oligonucleotide Duplex Reporter-Transcription Factor Complexes.  Bioconjugate Chem. 20, 1444–1448

Xu J, Li X, Lian JB, Ayers DC, Song J (2009) Sustained and localized in vitro release of BMP-2/7, RANKL, and tetracycline from FlexBone, an elastomeric osteoconductive bone substitute.  J Orthop Res. 27, 1306-1311.

Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX (2009) Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis.  Chem Biol Drug Des74, 234-45.

Su J, Iomdina E, Tarutta E, Ward B, Song J, Wildsoet CF (2009) Effects of poly(2-hydroxyethyl methacrylate) and poly(vinyl-pyrrolidone) hydrogel implants on myopic and normal chick sclera. J. Exp. Eye Res.  88 (3), 445-457.

Harwood KR and Miller SC (2009) Leveraging a small-molecule modification to enable the photoactivation of rho GTPases.  Chembiochem10, 2855-2857.

Song J, Xu J, Filion T, Saiz E, Tomsia AP, Lian JB, Stein GS, Ayers DC and Bertozzi CR. (2009)Elastomeric high-mineral content hydrogel-hydroxyapatite composites for orthopedic applications.  J. Biomed. Mater. Res. 89A (4), 1098-1107.

Mruk K and Kobertz WR (2009) Discovery of a Novel Activator of KCNQ1-KCNE1 K+ Channel Complexes.PLoS ONE 4, e4236.

Querol M, Bogdanov A Jr. (2008) Environment-sensitive and enzyme-sensitive MR contrast agents. Handb Exp Pharmacol Pt 2185, 37-57.

Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH and Wolfe, S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell.  133, 1277-1289.

O'Brien K, Matlin AJ, Lowell AM and Moore MJ (2008) The Biflavonoid Isoginkgetin Is a General Inhibitor of Pre-mRNA Splicing.  J Biol Chem. 283, 33147-33154.

Zhang S, Metelev V, Tabatadze D, Zamecnik P and Bogdanov A Jr. (2008) Near-infrared fluorescent oligodeoxyribonucleotide reporters for sensing NF-kappaB DNA interactions in vitro.  Oligonucleotides18, 235-243.

Meng X, Noyes MB, Zhu LJ, Lawson ND, and Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases.  Nat Biotechnol. 26, 695-701

Morin TJ and Kobertz WR (2008)  Tethering chemistry and K+ channels.  J Biol Chem. 283, 25105-25109.

Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM and Tidor B  (2008)  HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.  J Am Chem Soc. 130, 6099-6113.

Zhang S, Metelev V, Tabatadze D, Zamecnik PC and Bogdanov A Jr. (2008) Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein-DNA interactions.  Proc Natl Acad Sci USA. 105, 4156-4161.

Morin TJ and Kobertz WR (2008) Counting Membrane-embedded KCNE β-subunits in Functioning K+ Channel Complexes. Proc Natl Acad Sci USA. 105, 1478-1482.

Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH  and Wolfe SA (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.  Nucleic Acids Res. 36, 2547-2560.

Bhunia AK and Miller SC (2007) Labeling Tetracysteine-Tagged Proteins with a SplAsH of Color: A Modular Approach to Bis-Arsenical FluorophoresChemBioChem8, 1642-1645.

Querol M, Bennett DG, Sotak C, Kang, HW and Bogdanov A Jr. (2007) A Paramagnetic Contrast Agent for Detecting Tyrosinase ActivityChemBioChem8, 1637-1641.

Meng X, Thibodeau-Beganny S, Jiang T, Joung JK and Wolfe SA (2007) Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based methodNucleic Acids Res. 35, e81.

Kaufman JD, Song J and Klapperich CM (2007) Nanomechanical analysis of bone tissue engineering scaffoldsJ Biomed Mater Res81A, 611-623.

Chellappan S, Reddy K, Ali A, Altman MD, Nalam M, Cao H, Kairys V, Fernandes MX, Tidor B, Rana TM, Schiffer CA and Gilson M (2007) Design of Mutation-Resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis. Chem Biol Drug Des69, 298-313.

Robb GB and Rana TM (2007) RNA Helicase A Interacts with RISC in Human Cells and Functions in RISC LoadingMol Cell. 26, 523-537.

Morin TJ and Kobertz WR (2007) A Derivatized Scorpion Toxin Reveals the Functional Output of Heteromeric KCNQ1-KCNE K+ Channel ComplexesACS Chem Biol2, 469-473.

Baigude H, McCarroll J, Yang CS, Swain PM and Rana TM (2007) Design and creation of new nanomaterials for therapeutic RNAi. ACS Chem Biol. 2, 237-241.

Bogdanov A Jr., Kang HW, Querol M, Pretorius PH and Yudina A (2007) Synthesis and testing of a binary catalytic system for imaging of signal amplification in vivoBioconjug Chem18, 1123-1130.