Publications

• Ruble, B. K.; Yeldell, S. B.; Dmochowski, I. J. J. Inorg. Biochem. 2015. http://dx.doi.org/10.1016/j.jinorgbio.2015.03.010

• Wang, Y.; Dmochowski, I. Chem. Commun. 2015, 4 (8), 1166–1169. http://dx.doi.org/10.1039/C5CC01826A

• Riggle, B. A.; Wang, Y.; Dmochowski, I. J. J. Am. Chem. Soc. 2015. http://dx.doi.org/10.1021/jacs.5b01938

• Griepenburg, J. C.; Rapp, T. L.; Carroll, P. J.; Eberwine, J.; Dmochowski, I. J. Chem. Sci. 2015, 6, 2342–2346. http://dx.doi.org/10.1039/C4SC03990D

• Griepenburg, J. C.; Sood, N.; Vargo, K. B.; Williams, D.; Rawson, J.; Therien, M. J.; Hammer, D. A; Dmochowski, I. J. Langmuir 2014. http://dx.doi.org/10.1021/la5036689

• Khan, N. S.; Riggle, B. A.; Seward, G. K.; Bai, Y.; Dmochowski, I. J. Bioconjug. Chem. 2014. http://dx.doi/org/10.1021/bc5005526

• Bai, Y.; Wang, Y.; Goulian, M.; Driks, A.; Dmochowski, I. J. Bacterial spore detection and analysis using hyperpolarized ¹²⁹Xe chemical exchange saturation transfer (Hyper-CEST) NMR. Chem. Sci. 2014. http://dx.doi.org/10.1039/C4SC01190B

• Taratula, O.; Bai, Y.; D’Antonio, E. L.; Dmochowski, I. J. Enantiopure cryptophane-¹²⁹Xe nuclear magnetic resonance biosensors targeting carbonic anhydrase. Supramol. Chem. 2014, 1–8. http://dx.doi.org/10.108/10610278.2014.906601

• Lovatt, D.; Ruble, B. K.; Lee, J.; Dueck, H.; Kim, T. K.; Fisher, S.; Francis, C.; Spaethling, J. M.; Wolf, J. a; Grady, M. S.; Ulyanova, A. V; Yeldell, S. B.; Griepenburg, J. C.; Buckley, P. T.; Kim, J.; Sul, J.-Y.; Dmochowski, I. J.; Eberwine, J. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat. Methods 2014, 1–10. http://dx.doi.org/10.1038/nmeth.2804

• Cheung-Lau, J.C.; Liu, D.; Pulsipher, K.W.; Liu, W.; Dmochowski, I.J. Engineering a well-ordered, functional protein-gold nanoparticle assembly. J. Inorg. Biochem. 2014, 130, 59-68. http://dx.doi.org/10.1016/j.jinorgbio.2013.10.003

• Liao, Z.; Hsieh, W.-T.; Baumgart, T.; Dmochowski, I.J.; Measuring interactions between polydimethylsiloxane and serum proteins at the air-water interface. Langmuir 2013, 29 (30), 9420-9427. http://dx.doi.org/10.1021/la401619s

• Griepenburg, J. C.; Ruble, B. K.; Dmochowski, I. J., Caged oligonucleotides for bidirectional photomodulation of let-7 miRNA in zebrafish embryos. Bioorganic and Medicinal Chemistry 2013, 21 (20), 6198-6204. http://dx.doi.org/10.1016/j.bmc.2013.04.082

• Emerson, D. J.; Weiser, B. P.; Psonis, J.; Liao, Z.; Taratula, O.; Fiamengo, A.; Wang, X.; Sugasawa, K.; Smith Iii, A. B.; Eckenhoff, R. G.; Dmochowski, I. J., Direct modulation of microtubule stability contributes to anthracene general anesthesia. Journal of the American Chemical Society 2013, 135 (14), 5389-5398. http://dx.doi.org/10.1021/ja311171u

• Bai, Y.; Hill, P. A.; Dmochowski, I. J., Utilizing a water-soluble cryptophane with fast xenon exchange rates for picomolar sensitivity NMR measurements. Analytical Chemistry 2012, 84 (22), 9935-9941. http://dx.doi.org/10.1021/ac302347y

• Laureano-Perez, L.; Colle, R.; Jacobson, D. R.; Fitzgerald, R.; Khan, N. S.; Dmochowski, I. J., A novel application for 222Rn emanation standards: Radon-cryptophane host chemistry. Applied Radiation and Isotopes 2012, 70 (9), 1997-2001. http://dx/doi.org/10.1016/j.apradiso.2012.02.099

• Taratula, O.; Kim, M. P.; Bai, Y.; Philbin, J. P.; Riggle, B. A.; Haase, D. N.; Dmochowski, I. J., Synthesis of enantiopure, trisubstituted cryptophane - A derivatives. Organic Letters 2012, 14 (14), 3580-3583. http://dx.doi.org/10.1021/ol300943w

• Emerson, D. J.; Liao, Z.; Eckenhoff, R. G.; Dmochowski, I. J., A novel fluorescent general anesthetic enables imaging of sites of action in vivo. Anesthesiology 2012, 116 (6), 1363. http://dx.doi.org/10.1097/ALN.0b013e31824cb4b1

• Bu, W.; Liu, R.; Cheung-Lau, J. C.; Dmochowski, I. J.; Loll, P. J.; Eckenhoff, R. G., Ferritin couples iron and fatty acid metabolism. FASEB Journal 2012, 26 (6), 2394-2400. http://dx.doi.org/10.1096/fj.11-198853

• Liu, R.; Bu, W.; Xi, J.; Mortazavi, S. R.; Cheung-Lau, J. C.; Dmochowski, I. J.; Loll, P. J., Beyond the detergent effect: A binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin. Acta Crystallographica Section D: Biological Crystallography 2012, 68 (5), 497-504. http://dx.doi.org/10.1107/S0907444912002740

• Ruble, B. K.; Richards, J. L.; Cheung-Lau, J. C.; Dmochowski, I. J., Mismatch discrimination and efficient photomodulation with split 10-23 DNAzymes. Inorganica Chimica Acta 2012, 380 (1), 386-391. http://dx.doi.org/10.1016/j.ica.2011.10.068

• Liao, Z.; Lampe, J. W.; Ayyaswamy, P. S.; Eckmann, D. M.; Dmochowski, I. J., Protein assembly at the air-water interface studied by fluorescence microscopy. Langmuir 2011, 27 (21), 12775-12781. http://dx.doi.org/10.1021/la203053g

• Kamat, N. P.; Liao, Z.; Moses, L. E.; Rawson, J.; Therien, M. J.; Dmochowski, I. J.; Hamme, D. A., Sensing membrane stress with near IR-emissive porphyrins. Proceedings of the National Academy of Sciences of the United States of America 2011, 108 (34), 13984-13989. http://dx.doi.org/10.1073/pnas.1102125108

• Jacobson, D. R.; Khan, N. S.; Colle, R.; Fitzgerald, R.; Laureano-Perez, L.; Bai, Y.; Dmochowski, I. J., Measurement of radon and xenon binding to a cryptophane molecular host. Proceedings of the National Academy of Sciences of the United States of America 2011, 108 (27), 10969-10973. http://dx.doi.org/10.1073/pnas.1105227108

• Seward, G. K.; Bai, Y.; Khan, N. S.; Dmochowski, I. J., Cell-compatible, integrin-targeted cryptophane- 129Xe NMR biosensors. Chemical Science 2011, 2 (6), 1103-1110. http://dx.doi.org/10.1039/c1sc00041a

• Taratula, O.; Hill, P. A.; Bai, Y.; Khan, N. S.; Dmochowski, I. J., Shorter synthesis of trifunctionalized cryptophane - A derivatives. Organic Letters 2011, 13 (6), 1414-1417. http://dx.doi.org/10.1021/ol200088f

• Khan, N. S.; Perez-Aguilar, J. M.; Kaufmann, T.; Hill, P. A.; Taratula, O.; Lee, O. S.; Carroll, P. J.; Saven, J. G.; Dmochowski, I. J., Multiple hindered rotators in a gyroscope-inspired tribenzylamine hemicryptophane. Journal of Organic Chemistry 2011, 76 (5), 1418-1424. http://dx.doi.org/10.1021/jo102480s

• Taratula, O.; Hill, P. A.; Khan, N. S.; Carroll, P. J.; Dmochowski, I. J., Crystallographic observation of 'induced fit' in a cryptophane host-guest model system. Nature Communications 2010, 1 (9). http://dx.doi.org/10.1038/ncomms1151

• Kamat, N. P.; Robbins, G. P.; Rawson, J.; Therien, M. J.; Dmochowski, I. J.; Hammer, D. A., A generalized system for photoresponsive membrane rupture in polymersomes. Advanced Functional Materials 2010, 20 (16), 2588-2596. http://dx.doi/org/10.1002/adfm.201000659

• Lampe, J. W.; Liao, Z.; Dmochowski, I. J.; Ayyaswamy, P. S.; Eckmann, D. M., Imaging macromolecular interactions at an interface. Langmuir 2010, 26 (4), 2452-2459. http://dx.doi.org/10.1021/la903703u

• Richards, J. L.; Seward, G. K.; Wang, Y. H.; Dmochowski, I. J., Turning the 10-23 DNAzyme on and off with light. ChemBioChem 2010, 11 (3), 320-324. http://dx.doi.org/10.1002/cbic.200900702

• Taratula, O.; Dmochowski, I. J., Functionalized 129Xe contrast agents for magnetic resonance imaging. Current Opinion in Chemical Biology 2010, 14 (1), 97-104. http://dx.doi.org/10.1016/j.cbpa.2009.10.009

• Dmochowski, I., Xenon out of its shell. Nature chemistry 2009, 1 (3), 250. http://dx.doi.org/10.1038/nchem.230

• Swift, J.; Butts, C. A.; Cheung-Lau, J.; Yerubandi, V.; Dmochowski, I. J., Efficient Self-Assembly of Archaeoglobus fulgidus ferritin around metallic cores. Langmuir 2009, 25 (9), 5219-5225. http://dx.doi.org/10.1021/la8040743

• Butts, C. A.; Xi, J.; Brannigan, G.; Saad, A. A.; Venkatachalan, S. P.; Pearce, R. A.; Klein, M. L.; Eckenhoff, R. G.; Dmochowski, I. J., Identification of a fluorescent general anesthetic, 1-aminoanthracene. Proceedings of the National Academy of Sciences of the United States of America 2009, 106 (16), 6501-6506. http://dx.doi.org/10.1073/pnas.0810590106

• Robbins, G. P.; Jimbo, M.; Swift, J.; Therien, M. J.; Hammer, D. A.; Dmochowski, I. J., Photoinitiated destruction of composite Porphyrin-Protein polymersomes. Journal of the American Chemical Society 2009, 131 (11), 3872-3874. http://dx.doi.org/10.1021/ja808586q

• Aru Hill, P.; Wei, Q.; Troxler, T.; Dmochowski, I. J., Substituent effects on xenon binding affinity and solution behaviour of water-soluble cryptophanes. Journal of the American Chemical Society 2009, 131 (8), 3069-3077. http://dx.doi.org/10.1021/ja8100566

• Chambers, J. M.; Hill, P. A.; Aaron, J. A.; Han, Z.; Christiansen, D. W.; Kuzma, N. N.; Dmochowski, I. J., Cryptophane xenon-129 nuclear magnetic resonance biosensors targeting human carbonic anhydrase. Journal of the American Chemical Society 2009, 131 (2), 563-569. http://dx.doi.org/10.1021/ja806092w

• Butts, C. A.; Swift, J.; Kang, S. G.; Di Costanzo, L.; Christiansen, D. W.; Saven, J. G.; Dmochowski, I. J., Directing noble metal ion chemistry within a designed ferritin protein. Biochemistry 2008, 47 (48), 12729-12739. http://dx.doi.org/10.1021/bi8016735

• Richards, J. L.; Tang, X.; Turetsky, A.; Dmochowski, I. J., RNA bandages for photoregulating in vitro protein synthesis. Bioorganic and Medicinal Chemistry Letters 2008, 18 (23), 6255-6258. http://dx.doi.org/10.1016/j.bmcl.2008.09.093

• Seward, G. K.; Wei, Q.; Dmochowski, I. J., Peptide-mediated cellular uptake of cryptophane. Bioconjugate Chemistry 2008, 19 (11), 2129-2135. http://dx.doi.org/10.1021/bc8002265

• Aaron, J. A.; Chambers, J. M.; Jude, K. M.; Di Costanzo, L.; Dmochowski, I. J.; Christianson, D. W., Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II. Journal of the American Chemical Society 2008, 130 (22), 6942-6943. http://dx.doi.org/10.1021/ja802214x

• Tang, X.; Swaminathan, J.; Gewirtz, A. M.; Dmochowski, I. J., Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides. Nucleic Acids Research 2008, 36 (2), 559-569. http://dx.doi.org/10.1093/nar/gkm1029

• Zhang, L.; Swift, J.; Butts, C. A.; Yerubandi, V.; Dmochowski, I. J., Structure and activity of apoferritin-stabilized gold nanoparticles. Journal of Inorganic Biochemistry 2007, 101 (11-12), 1719-1729. http://dx.doi.org/10.1016/j.jinorgbio.2007.07.023

• Hill, P. A.; Wei, Q.; Eckenhoff, R. G.; Dmochowski, I. J., Erratum: Thermodynamics of xenon binding to cryptophane in water and human plasma (Journal of the American Chemical Society (2007) 129, (9262-9263)). Journal of the American Chemical Society 2007, 129 (37), 11662. http://dx.doi.org/10.1021/ja075845q

• Tang, X.; Maegawa, S.; Weinberg, E. S.; Dmochowski, I. J., Regulating gene expression in zebrafish embryos using light-activated, negatively charged peptide nucleic acids. Journal of the American Chemical Society 2007, 129 (36), 11000-11001. http://dx.doi.org/10.1021/ja073723s

• Hill, P. A.; Wei, Q.; Eckenhoff, R. G.; Dmochowski, I. J., Thermodynamics of xenon binding to cryptophane in water and human plasma. Journal of the American Chemical Society 2007, 129 (30), 9262-9263. http://dx.doi.org/10.1021/ja072965p

• Dmochowski, I. J.; Tang, X., Taking control of gene expression with light-activated oligonucleotides. BioTechniques 2007, 43 (2), 161-171. http://dx.doi.org/10.2144/000112519

• Dmochowski, I.; Tang, X., Probing expression. Organic & biomolecular chemistry 2007, 5 (3). http://dx.doi.org/10.1039/C3OB41467A

• Tang, X.; Dmochowski, I. J., Regulating gene expression with light-activated oligonucleotides. Molecular BioSystems 2007, 3 (2), 100-110. http://dx.doi.org/10.1039/b614349k

• Tang, X. J.; Dmochowski, I. J., Synthesis of light-activated antisense oligodeoxynucleotide. Nature Protocols 2007, 1 (6), 3041-3048. http://dx.doi.org/10.1038/nprot.2006.462

• Wei, Q.; Seward, G. K.; Hill, P. A.; Patton, B.; Dimitrov, I. E.; Kuzma, N. N.; Dmochowski, I. J., Designing 129Xe NMR biosensors for matrix metalloproteinase detection. Journal of the American Chemical Society 2006, 128 (40), 13274-13283. http://dx.doi.org/10.1021/ja0640501

• Swift, J.; Wehbi, W. A.; Kelly, B. D.; Stowell, X. F.; Saven, J. G.; Dmochowski, I. J., Design of functional ferritin-like proteins with hydrophobic cavities. Journal of the American Chemical Society 2006, 128 (20), 6611-6619. http://dx.doi.org/10.1021/ja057069x

• Tang, X.; Dmochowski, I. J., Controlling RNA digestion by RNase H with a light-activated DNA hairpin. Angewandte Chemie - International Edition 2006, 45 (21), 3523-3526. http://dx.doi.org/10.1002/anie.200600954

• Agadjanian, H.; Weaver, J. J.; Mahammed, A.; Rentsendorj, A.; Bass, S.; Kim, J.; Dmochowski, I. J.; Margalit, R.; Gray, H. B.; Gross, Z.; Medina-Kauwe, L. K., Specific delivery of corroles to cells via noncovalent conjugates with viral proteins. Pharmaceutical Research 2006, 23 (2), 367-377. http://dx.doi.org/10.1007/s11095-005-9225-1

• Tang, X.; Richards, J. L.; Peritz, A. E.; Dmochowski, I. J., Photoregulation of DNA polymerase I (Klenow) with caged fluorescent oligodeoxynucleotides. Bioorganic and Medicinal Chemistry Letters 2005, 15 (23), 5303-5306. http://dx.doi.org/10.1016/j.bmcl.2005.08.058

• Tang, X.; Dmochowski, I. J., Phototriggering of caged fluorescent oligodeoxynucleotides. Organic Letters 2005, 7 (2), 279-282. http://dx.doi.org/10.1021/ol047729n

• Arnone, M. I.; Dmochowski, I. J.; Gache, C., Using reporter genes to study cis-regulatory elements. 2004; Vol. 2004, pp 621-652. http://dx.doi.org/10.1016/S0091-679X(04)74025-X

• Dunn, A. R.; Dmochowski, I. J.; Winkler, J. R.; Gray, H. B., Nanosecond photoreduction of cytochrome P450cam by channel-specific Ru-diimine electron tunneling wires. Journal of the American Chemical Society 2003, 125 (41), 12450-12456. http://dx.doi.org/10.1021/ja0294111

• Dmochowski, I. J.; Dunn, A. R.; Wilker, J. J.; Crane, B. R.; Green, M. T.; Dawson, J. H.; Sligar, S. G.; Winkler, J. R.; Gray, H. B., Sensitizer-linked substrates and ligands: Ruthenium probes of cytochrome P450 structure and mechanism. 2002; Vol. 357, pp 120-133. http://dx.doi.org/10.1016/S0076-6879(02)57672-2

• Dmochowski, I. J.; Dmochowski, J. E.; Oliveri, P.; Davidson, E. H.; Fraser, S. E., Quantitative imaging of cis-regulatory reporters in living embryos. Proceedings of the National Academy of Sciences of the United States of America 2002, 99 (20), 12895-12900. http://dx.doi.org/10.1073/pnas.202483199

• Dunn, A. R.; Dmochowski, I. J.; Bilwes, A. M.; Gray, H. B.; Crane, B. R., Probing the open state of cytochrome P450cam with ruthenium-linker substrates. Proceedings of the National Academy of Sciences of the United States of America 2001, 98 (22), 12420-12425. http://dx.doi.org/10.1073/pnas.221297998

• Bendix, J.; Dmochowski, I. J.; Gray, H. B.; Mahammed, A.; Simkhovich, L.; Gross, Z., Evidence for the formation of a Ru(III)-Ru(III) bond in a ruthenium corrole homodimer. Angewandte Chemie - International Edition 2000, 39 (22), 4051-4053. http://dx.doi.org/10.1002/1521-3773(20001117)39:22<4051::AID-ANIE4051>3.0.CO;2-A

• Dmochowski, I. J.; Winkler, J. R.; Gray, H. B., Enantiomeric discrimination of Ru-substrates by cytochrome P450(cam). Journal of Inorganic Biochemistry 2000, 81 (3), 221-228. http://dx.doi.org/10.1016/S0162-0134(00)00111-2

• Dmochowski, I. J.; Crane, B. R.; Wilker, J. J.; Winkler, J. R.; Gray, H. B., Optical detection of cytochrome P450 by sensitizer-linked substrates. Proceedings of the National Academy of Sciences of the United States of America 1999, 96 (23), 12987-12990. http://dx.doi.org/10.1073/pnas.96.23.12987

• Wilker, J. J.; Dmochowski, I. J.; Dawson, J. H.; Winkler, J. R.; Gray, H. B., Substrates for rapid delivery of electrons and holes to buried active sites in proteins. Chemtracts 1999, 12 (8), 565-569.

• Wilker, J. J.; Dmochowski, I. J.; Dawson, J. H.; Winkler, J. R.; Gray, H. B., Substrates for rapid delivery of electrons and holes to buried active sites in proteins. Angewandte Chemie - International Edition 1999, 38 (1-2), 90-92. http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2<89::AID-ANIE89>3.0.CO;2-R

• Wilker, J. J.; Dmochowski, I. J.; Dawson, J. H.; Winkler, J. R.; Gray, H. H., Production of high valent iron-oxo species in cytochrome P450-CAM by electron transfer through protein substrates. FASEB Journal 1997, 11 (9).

• Rego, J. A.; Kumar, S.; Dmochowski, I. J.; Ringsdorf, H., Synthesis of novel mixed tail triphenylene discotic liquid crystals - The search for higher order. Chemical Communications 1996, (9), 1031-1032. http://dx.doi.org/10.1039/CC9960001031

Patents

• I.J. Dmochowski, B.R. Crane, A.R. Dunn, H.B. Gray, J.J. Wilker, J.R. Winkler, Detection of biomolecules by sensitizer-linked substrates, serial number 10/031,532; patent number 7,105,310, issued 9/12/06.

• I.J. Dmochowski, P.A. Hill, Q. Wei, N.N. Kuzma, 129Xe biosensors and their use, P-9049-USP, provisional filed 08/27/06, U.S. patent application filed 8/6/07.

• I.J. Dmochowski, X. Tang, Photocleavable oligonucleotide and uses thereof, filed 12/04/06, provisional filed 11/27/07, U.S. patent application filed 11/08.

• I.J. Dmochowski, P.A. Hill, Q. Wei, J.L. Chambers, Tri-functionalized cryptophanes and their use, provisional filed 07/07/08, U.S. patent application filed 7/07/09.

• M. Jimbo, G. Robbins, N. Kamat, I.J. Dmochowski, M.J. Therien, D. Hammer, Polymer vesicles for selective electromagnetic energy-induced delivery, U.S. patent application #12/548,801 filed 8/27/09.

Prominent Citations of Research

• University of Pennsylvania Gazette, highlight featuring annual research accomplishments at UPenn, citing fluorescent anesthetic studies, ref. 32.

• In Science Daily, April 8, 2009, “New model for drug discovery with fluorescent anesthetic demonstrated” featuring ref. 32.

• In Nature Chemistry, Jan. 2009 “Research Highlight” on homepage, “Biosensors: The Xe-Factor”, article by Gavin Armstrong featuring ref. 28.

• On ACS home page, “News and Research” during week of Nov. 1, 2008, highlighted work on xenon biosensors published in ref. 25.

• In ACS Chemical Biology, 2, 646-648, Oct. 2007 “Point of View” titled “Yin-Yang Ways of Controlling Gene Expression Are Now in Our Hands” by Hitoshi Okamoto featuring ref. 22.

• Faculty of 1000 Biology recognition from Edward Stiefel, June 2006, featuring ref. 13.