CURRICULUM VITAE
`University of Idaho
`
`DATE: Sep-18
`
`OFFICE PHONE: 208-885-0108
`FAX: 208-885-6173
`EMAIL: hrdlicka@uidaho.edu
`
`NAME: Patrick J. Hrdlicka
`
`RANK: Professor
`
`DEPARTMENT: Chemistry
`
`
`
`OFFICE LOCATION AND CAMPUS ZIP:
`University of Idaho, Department of Chemistry
`875 Perimeter Drive MS 2343 (Renfrew Hall 307)
`Moscow, ID 83844-2343, USA
`
`WEB: http://www.webpages.uidaho.edu/~hrdlicka/index.htm
`
`DATE OF FIRST EMPLOYMENT AT UI: August 2006
`
`DATE OF TENURE: July 2011
`
`IMMIGRATION STATUS: Permanent resident (green card holder)
`
`PROFESSIONAL PREPARATION:
`
`2006 Ph.D (Chemistry), Univ. Southern Denmark, Odense, Denmark (supervisor: Jesper Wengel)
`2004 M.Sc (Chemistry), Univ. Southern Denmark, Odense, Denmark (supervisor: Jesper Wengel)
`2000 B.Sc (Chemistry), Univ. Southern Denmark, Odense, Denmark (supervisor: JJL Iversen, deceased)
`
`EXPERIENCE:
`
`Professor, Dept. Chemistry, Univ. Idaho
`2017-
`2011-2017 Associate Professor, Dept. Chemistry, Univ. Idaho
`2006-2011 Assistant Professor, Dept. Chemistry, Univ. Idaho
`
`2013-2016 Affiliate Faculty, Dept. Biological Sciences, Univ. Idaho
`2011-2014 Adjunct Faculty, Dept. Chemistry, Washington State University
`2006-2013 Affiliate Faculty, Neuroscience Graduate Program, Univ. Idaho
`
`Retained as a subject matter expert on three litigations pertaining to DNA sequencing
`2016-
`2016-2017 Retained as a subject matter expert on a litigation pertaining to siRNA
`2011-2015 Consultant for Minitube of America (now MOFA Global)
`2011-2012 Consultant for ISIS Pharmaceuticals Inc (now Ionis Pharmaceuticals)
`
`SCHOLARSHIP ACCOMPLISHMENTS:
`
`Publications:
`62 peer-reviewed articles and reviews (according to Google Scholar: 1350 citations, h-index = 21, i10-index = 40);
`eight patent applications (three issued); two book chapters; 35 published conference proceedings/abstracts; one
`published book review.
`
`Peer Reviewed Journal Articles and Reviews:
`
`[62] P. J. Hrdlicka* and S. Karmakar. 25 Years and still going strong: 2′-O-(Pyren-1-yl)methylribonucleotides
`- Versatile building blocks for applications in molecular biology, diagnostics and materials science. Org.
`Biomol. Chem., 2017, 15, 9760-9774.
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`[61] S. Karmakar, D. C. Guenther, B. C. Gibbons and P. J. Hrdlicka*. Recognition of mixed-sequence DNA
`using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-
`functionalized RNA monomers. Org. Biomol. Chem., 2017, 15, 9362-9371.
`
`[60] M. Kaura and P. J. Hrdlicka*. Efficient discrimination of single nucleotide polymorphisms (SNPs) using
`oligonucleotides modified with C5-pyrene-functionalized DNA and flanking Locked Nucleic Acid (LNA)
`monomers. Chem. Asian J., 2016, 11, 1366-1369.
`
`[59] B. A. Anderson and P. J. Hrdlicka*. Merging two strategies for mixed-sequence recognition of double-
`stranded DNA: Pseudocomplementary Invader probes. J. Org. Chem., 2016, 81, 3335-3346.
`
`[58] S. Geny, P. M. D Moreno, T. Krzywkowski, N. K. Andersen, A. J. Isse, A. M. El-Madani, C. Lou, Y. V.
`Pabon, O. Gissberg, B. A. Anderson, E. M. Zaghloul, R. Zain, P. J. Hrdlicka, P. T. Jørgensen, M. Nilsson, K.
`E. Lundin, E. B. Pedersen, J. Wengel, and C. I. E. Smith. Next generation bis-locked nucleic acids with
`stacking linker and 2’-glycylamino-LNA show enhanced invasion into supercoiled duplex DNA. Nucleic
`Acids Res., 2016, 44, 2007-2019.
`
`[57] D. G. Singleton, R. Hussain, G. Siligardi, P. Kumar, P. J. Hrdlicka, N. Berova and E. Stulz*. Increased
`duplex stabilization in porphyrin-LNA zipper arrays with structure dependent excitonic coupling. Org.
`Biomol. Chem., 2016, 14, 149-157.
`
`[56] D. C. Guenther, S. Karmakar and P. J. Hrdlicka*. Bulged Invader probes: Activated duplexes for mixed-
`sequence dsDNA recognition with improved thermodynamic and kinetic profiles. Chem. Commun., 2015, 51,
`15051-15054.
`
`[55] B. A. Anderson, S. Karmakar and P. J. Hrdlicka*. Mixed-sequence recognition of double-stranded DNA
`using enzymatically stable phosphorothioate Invader probes. Molecules, 2015, 20, 13780-13793.
`
`[54] B. A. Anderson and P. J. Hrdlicka*. Synthesis and characterization of oligodeoxyribonucleotides
`modified with 2′-thio-2′-deoxy-2′-S-(pyren-1-yl)methyluridine. Bioorg. Med. Chem. Lett., 2015, 25, 3999-
`4004.
`
`[53] D. C. Guenther, G. H. Anderson, S. Karmakar, B. A. Anderson, B. A. Didion, W. Guo, J. P. Verstegen
`and P. J. Hrdlicka*. Invader probes: Harnessing the energy of intercalation to facilitate recognition of
`chromosomal DNA for diagnostic applications. Chem. Sci., 2015, 6, 5006-5015.
`
`[52] M. Kaura and P. J. Hrdlicka*. Locked Nucleic Acid (LNA) induced effect on hybridization and
`fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA
`monomers. Org. Biomol. Chem., 2015, 13, 7236-7247.
`
`[51] B. A. Anderson, J. J. Onley and P. J. Hrdlicka*. Recognition of double-stranded DNA using energetically
`activated duplexes modified with N2′-pyrene-, perylene-, or coronene-functionalized 2′-N-methyl-2′-amino-
`DNA monomers. J. Org. Chem., 2015, 80, 5395-5406 (Featured Article).
`
`[50] S. Karmakar, A. S. Madsen, D. C. Guenther, B. C. Gibbons and P. J. Hrdlicka*. Recognition of double-
`stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-
`functionalized O2'-alkylated RNA monomers. Org. Biomol. Chem., 2014, 12, 7758-7773.
`
`[49] B-A. F. Kengne, S. Karmakar, M. Kaura, G. Corti, V. V. R. Sai, I. B. Niraula, A. Larin, J. Hall, D.
`Sowell, P. J. Hrdlicka, V. Dobrokhotov and D. N. McIlroy*. Self-assembled monolayers of thiols adsorbed on
`Au/ZnO-functionalized silica nanosprings: Photoelectron spectroscopy-analysis and detection of vaporized
`explosives. ACS Appl. Mater. Interfaces, 2014, 6, 13355-13366.
`
`[48] D. C. Guenther, P. Kumar, B. A. Anderson and P. J. Hrdlicka*. C5-Amino acid functionalized LNA:
`Positively poised for antisense applications. Chem. Commun., 2014, 50, 9007-9009.
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`[47] M. Kaura, P. Kumar and P. J. Hrdlicka*. Synthesis, hybridization characteristics and fluorescence
`properties of oligonucleotides modified with nucleobase-functionalized LNA (Locked Nucleic Acid)
`adenosine and cytidine monomers. J. Org. Chem., 2014, 79, 6256-6268.
`
`[46] M. Kaura, D. C. Guenther and P. J. Hrdlicka*. Carbohydrate-functionalized Locked Nucleic Acids
`(LNAs): Oligonucleotides with extraordinary binding affinity, target specificity and enzymatic stability. Org.
`Lett., 2014, 16, 3308-3311.
`
`[45] P. Kumar, B. Bharal, B. A. Anderson, D. C. Guenther, M. E. Østergaard, P. K. Sharma and P. J.
`Hrdlicka*. C5-Alkynyl functionalized -L-LNA: Synthesis, thermal denaturation experiments and enzymatic
`stability. J. Org. Chem., 2014, 79, 5062-5073.
`
`[44] P. Kumar, M. E. Østergaard, B. Bharal, B. A. Anderson, D. C. Guenther, M. Kaura, D. J. Raible, P. K.
`Sharma and P. J. Hrdlicka*. Synthesis and biophysical properties of C5-functionalized LNA (Locked Nucleic
`Acid). J. Org. Chem., 2014, 79, 5047-5061.
`
`[43] N. K. Andersen, B. A. Anderson, J. Wengel and P. J. Hrdlicka*. Synthesis and characterization of
`oligodeoxyribonucleotides modified with 2′-amino--L-LNA adenine monomers – High-affinity targeting of
`single-stranded DNA. J. Org. Chem., 2013, 78, 12690-12702.
`
`[42] S. Karmakar, D. C. Guenther and P. J. Hrdlicka*. Recognition of mixed-sequence DNA duplexes: Design
`guidelines for Invaders based on 2′-O-(pyren-1-yl)methyl-RNA monomers. J. Org. Chem., 2013, 78, 12040-
`12048.
`
`[41] S. P. Sau, A. S. Madsen, P. Podbevsek, N. K. Andersen, T. S. Kumar, S. Andersen, R. L. Rathje, B. A.
`Anderson, D. C. Guenther, S. Karmakar, P. Kumar, J. Plavec, J. Wengel and P. J. Hrdlicka*. Identification
`and characterization of 2nd generation Invader LNAs for mixed-sequence recognition of double-stranded
`DNA. J. Org. Chem., 2013, 78, 9560-9570 (Featured Article).
`
`[40] B. Denn, S. Karmakar, D. C. Guenther and P. J. Hrdlicka*. Sandwich assay for mixed-sequence
`recognition of double-stranded DNA: Invader-based detection of targets specific to food pathogens. Chem.
`Commun., 2013, 49, 9851-9853.
`
`[39] B. A. Didion, S. Karmakar, D. C. Guenther, S. Sau, J. P. Verstegen and P. J. Hrdlicka*. Invaders:
`Recognition of double-stranded DNA using duplexes modified with interstrand zippers of 2′-O-(pyren-1-
`yl)methylribonucleotides. ChemBioChem, 2013, 14, 1534-1538.
`
`[38] S. Karmakar and P. J. Hrdlicka*. DNA strands with alternating incorporations of LNA and 2′-O-(pyren-
`1-yl)methyluridine: SNP-discriminating RNA detection probes. Chem. Sci., 2013, 4, 3447-3454.
`
`[37] M. Kaura, P. Kumar and P. J. Hrdlicka*. Synthesis and hybridization properties of oligonucleotides
`modified with 5-(1-aryl-1,2,3-triazol-4-yl)-2′-deoxyuridines. Org. Biomol. Chem., 2012, 10, 8575-8578 (Hot
`Communication).
`
`[36] S. P. Sau, P. Kumar, P. K. Sharma and P. J. Hrdlicka*. Fluorescent Intercalator Displacement
`Replacement (FIDR) assay: Determination of relative thermodynamic and kinetic parameters in triplex
`formation - A case study using triplex-forming LNAs. Nucleic Acids Res., 2012, 40, e162.
`
`[35] S. K. Rastogi,* C. M. Gibson, J. R. Branen, D. E. Aston, A. L. Branen and P. J. Hrdlicka*. DNA
`detection on lateral flow test strips: Enhanced signal sensitivity using LNA-conjugated gold nanoparticles.
`Chem. Commun, 2012, 48, 7714-7716.
`
`[34] G. Wang, M. R. Papasani, P. Cheguru, P. J. Hrdlicka and R. A. Hill*. Gold-peptide nanoconjugate
`cellular uptake is modulated by serum proteins. Nanomedicine: NBM, 2012, 8, 822-832.
`
`[33] S. P. Sau and P. J. Hrdlicka*. C2′-Pyrene-functionalized triazole-linked DNA: Universal hybridization to
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`DNA/RNA. J. Org. Chem., 2012, 77, 5-16 (Cover Article).
`[32] S. Karmakar, B. A. Anderson, R. L. Rathje, S. Andersen, T. Jensen, P. Nielsen and P. J. Hrdlicka*. High-
`affinity DNA-targeting using readily accessible mimics of N2′-functionalized 2′-amino-α-L-LNA. J. Org.
`Chem., 2011, 76, 7119-7131.
`
`[31] P. Kumar, M. E. Østergaard and P. J. Hrdlicka*. Preparation of C5-functionalized Locked Nucleic Acids
`(LNAs). Curr. Protocols Nucleic Acid Chem., 2011, 44, 4.43.1-4.43.22.
`
`[30] M. E. Østergaard, P. Kumar, B. Baral, D. C. Guenther, B. A. Anderson, F. M. Ytreberg, L. Deobald, A.
`J. Paszczynski, P. K. Sharma and P. J. Hrdlicka*. C5-Functionalized DNA, LNA and alpha-L-LNA: Improved
`positional control of polarity-sensitive fluorophores facilitates improved SNP-typing. Chem. Eur. J., 2011,
`17, 3157-3165.
`
`[29] M. E. Østergaard and P. J. Hrdlicka*. Pyrene-functionalized oligonucleotides and Locked Nucleic Acids
`(LNAs): Tools for fundamental research, diagnostics, and materials science. Chem. Soc. Rev., 2011, 40, 5771-
`5788 (150+ citations as of September 18).
`
`[28] V. V. R. Sai, D. Gangadean, I. Niraula, G. Corti, D. N. McIlroy, D. E. Aston, J. R. Branen and P. J.
`Hrdlicka*. Silica nanosprings coated with noble metal nanoparticles: Highly active SERS substrates. J. Phys.
`Chem. C., 2011, 115, 453-459.
`
`[27] M. E. Østergaard, J. Maiti, B. R. Babu, J. Wengel and P. J. Hrdlicka*. Glowing LNA as nucleic acid
`detection probes – Nucleobase analogs and insights into probe design. Bioorg. Med. Chem. Lett., 2010, 20,
`7265-7268.
`
`[26] R. N. Veedu,* H. R. Burri, P. Kumar, P. K. Sharma, P. J. Hrdlicka, B. Vester and J. Wengel. Polymerase-
`directed synthesis of C5-ethynyl Locked Nucleic Acids. Bioorg. Med. Chem. Lett, 2010, 22, 6565-6568.
`
`[25] M. E. Østergaard, P. Cheguru, M. R. Papasani, R. A. Hill* and P. J. Hrdlicka*. Glowing LNA – Brightly
`fluorescent probes for detection of nucleic acids in cells. J. Am. Chem. Soc. 2010, 132, 14221-14228.
`
`[24] M. E. Østergaard, D. C. Guenther, P. Kumar, B. Baral, L. Deobald, A. J. Paszczynski, P. K. Sharma and
`P. J. Hrdlicka*. Pyrene-functionalized triazole-linked 2′-deoxyuridines - Probes for discrimination of single
`nucleotide polymorphisms (SNPs). Chem. Commun., 2010, 4929-4931.
`
`[23] S. P. Sau, T. S. Kumar and P. J. Hrdlicka*. Invader LNA – Efficient targeting of short DNA duplexes.
`Org. Biomol. Chem., 2010, 8, 2028-2036.
`
`[22] M. E. Østergaard, P. Kumar, B. Baral, D. J. Raible, T. S. Kumar, B. A. Anderson, D. C. Guenther, L.
`Deobald, A. J. Paszczynski, P. K. Sharma and P. J. Hrdlicka*. C5-Functionalized LNA: Unparalleled
`hybridization properties and enzymatic stability. ChemBioChem, 2009, 10, 2740-2743.
`
`[21] S. P. Sau, P. Kumar, B. A. Anderson, M. E. Østergaard, L. Deobald, A. J. Paszczynski, P. K. Sharma and
`P. J. Hrdlicka*. Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA. Chem.
`Commun, 2009, 6756-6758.
`
`[20] S. K. Rastogi, N. N. Mishra, M. E. Østergaard, E. Cameron, B. Finaloski, P. J. Hrdlicka and W. C.
`Maki*. Hybridization study of PNA-DNA in liquid-solid phase for biosensor application. Anal. Lett., 2009,
`42, 2485-2495.
`
`[19] B. Baral, P. Kumar, B. A. Anderson, M. E. Østergaard. P. K. Sharma and P. J. Hrdlicka*. Optimized
`synthesis of [3-15N]-labeled uridine phosphoramidites. Tetrahedron Lett., 2009, 50, 5850-5852.
`
`[18] T. S. Kumar, M. E. Østergaard, P. K. Sharma, P. Nielsen, J. Wengel and P. J. Hrdlicka*. Parallel RNA-
`strand recognition by 2′-amino-β-L-LNA. Bioorg. Med. Chem. Lett., 2009, 19, 2396-2399.
`
`[17] J. W. Rigoli, M. E. Østergaard, K. M. Canady, D. C. Guenther and P. J. Hrdlicka*. Selective deacylation
`of peracylated ribonucleosides. Tetrahedron Lett., 2009, 50, 1751-1753.
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`[16] T. S. Kumar, A. S. Madsen, M. E. Østergaard, S. P. Sau, J. Wengel and P. J. Hrdlicka*. Functionalized
`2′-amino--L-LNA - Directed positioning of intercalators for DNA targeting. J. Org. Chem. 2009, 74, 1070-
`1081.
`
`[15] T. S. Kumar, P. Kumar, P. K. Sharma and P. J. Hrdlicka*. Optimized synthesis of LNA uracil
`nucleosides. Tetrahedron Lett., 2008, 49, 7168-7170.
`
`[14] T. S. Kumar, A. S. Madsen, M. E. Østergaard, J. Wengel* and P. J. Hrdlicka*. Nucleic acid structural
`engineering using pyrene functionalized 2′-amino-α-L-LNA monomers and abasic sites. J. Org. Chem. 2008,
`73, 7060-7066.
`
`[13] B. Vester, A. M. Boel, S. Lobedanz, B. R. Babu, M. Raunkjær, D. Lindegaard, Raunak, P. J. Hrdlicka, T.
`Højland, P. K. Sharma, T. S. Kumar, P. Nielsen and J. Wengel*. Chemically modified oligonucleotides with
`retained RNaseH response. Bioorg. Med. Chem. Lett. 2008, 18, 2296-2300.
`
`[12] T. Umemoto, P. J. Hrdlicka, B. R. Babu and J. Wengel*. Sensitive SNP dual-probe assays based on
`pyrene-functionalized 2′-amino-LNA: Lessons to be learned. ChemBioChem, 2007, 8, 2240-2248.
`
`[11] T. S. Kumar, J. Wengel and P. J. Hrdlicka*. 2′-N-(pyren-1-yl)acetyl-2′-amino--L-LNA: Synthesis and
`detection of single nucleotide mismatches in DNA and RNA targets. ChemBioChem, 2007, 8, 1122-1125.
`
`[10] A. S. Madsen, P. J. Hrdlicka, T. S. Kumar and J. Wengel*. Synthesis, nucleic acid hybridization
`properties and molecular modeling studies of conformationally restricted 3′-O,4′-C-methylene-linked -L-
`ribonucleotides. Carbohydr. Res. 2006, 341, 1398-1407.
`
`[9] T. S. Kumar, A. S. Madsen, J. Wengel and P. J. Hrdlicka*. Synthesis and hybridization studies of 2′-
`amino--L-LNA and a tetracyclic ‘Locked LNA’. J. Org. Chem. 2006, 71, 4188-4201.
`
`[8] P. J. Hrdlicka, T. S. Kumar and J. Wengel*. Synthesis and thermal denaturation studies of
`conformationally restricted 3′-C-ethynyl-3′-O,4′-C-methyleneribonucleotides. Eur. J. Org. Chem. 2005,
`5184-5188.
`
`[7] P. J. Hrdlicka, B. R. Babu, M. D. Sørensen, N. Harrit and J. Wengel*. Multilabeled pyrene-functionalized
`2′-amino-LNA probes for nucleic acid detection in homogenous fluorescence assays. J. Am. Chem. Soc. 2005,
`127, 13293-13299 (125 citations as of April 2018).
`
`[6] P. J. Hrdlicka, T. S. Kumar and J. Wengel*. Targeting of mixed sequence double-stranded DNA using
`pyrene-functionalized 2′-amino--L-LNA. Chem. Commun. 2005, 4279-4281.
`
`[5] B. R. Babu, P. J. Hrdlicka, C. J. McKenzie and J. Wengel*. Optimized DNA targeting using N,N-bis(2-
`pyridylmethyl)-β-alanyl 2′-Amino-LNA. Chem. Commun. 2005, 1705-1707.
`
`[4] P. J. Hrdlicka, N. K. Andersen, J. S. Jepsen, F. G. Hansen, K. F. Haselmann, C. Nielsen and J. Wengel*.
`Synthesis and biological evaluation of branched and conformationally restricted analogs of the anticancer
`compounds 3′-C-ethynyluridine (EUrd) and 3′-C-ethynylcytidine (ECyd). Bioorg. Med. Chem. 2005, 13,
`2597-2621.
`
`[3] P. J. Hrdlicka, J. S. Jepsen, C. Nielsen and J. Wengel*. Synthesis and biological evaluation of nucleobase-
`modified analogs of the anticancer compounds 3′-C-ethynyluridine (EUrd) and 3′-C-ethynylcytidine (ECyd).
`Bioorg. Med. Chem. 2005, 13, 1249-1260.
`
`[2] P. J. Hrdlicka, B. R Babu, M. D. Sørensen and J. Wengel*. Interstrand communication between 2′-N-
`(pyren-1-yl)methyl-2′-amino LNA monomers in nucleic acid duplexes: Directional control and signaling of
`full complementarity. Chem. Commun. 2004, 1478-1479.
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`[1] P. J. Hrdlicka, A. B. Sørensen, B. R. Poulsen, G. J. G. Ruijter, J. Visser and J. J. L. Iversen*.
`Characterization of nerolidol biotransformation based on indirect on-line estimation of biomass concentration
`and physiological state in batch cultures of Aspergillus niger. Biotechnol. Prog. 2004, 20, 368-376.
`
`Manuscripts Submitted for Review:
`
`N/A
`
`Refereed Book Chapters:
`
`[BC2] P. J. Hrdlicka* and Michael E. Østergaard. Fluorophore-functionalized Locked Nucleic Acids (LNAs)
`in DNA Conjugates and Sensors, RSC Biomolecular Science Series, edited by K. R. Brown and T. Brown
`(RSC Publishing, 2012), Vol. 26, 1-33.
`
`[BC1] D. Choi*, D. McIlroy, J. Nagler, E. Aston, P. J. Hrdlicka, K. Gustin, R. Hill, D. Stenkamp and J.
`Branen. 1-Dimensional silica structures and their applications to the biological sciences in Nanomaterials for
`the Life Sciences, Nanostructured Oxides, edited by C. Kumar (Wiley, 2009), Vol. 2, 83-108.
`
`Patent Applications:
`
`[PA8] B. Didion, P. J. Hrdlicka and J. Verstegen. Gender-specific identification of sperm cells and embryos
`using locked nucleic acid probes for gender-specific sequences. 2013, PCT WO 2013103713A1.
`
`[PA7] P. J. Hrdlicka. Embodiments of a probe and method for targeting nucleic acids. U.S. Patent No.
`9,885,082 (issued February 2018).
`
`[PA6] P. J. Hrdlicka and Sujay P. Sau. Universal DNA/RNA hybridization probes. Provisional patent
`application, Univ. Idaho, October 31, 2011.
`
`[PA5] P. J. Hrdlicka. Embodiments of a probe and method for targeting nucleic acids. Provisional patent
`application, Univ. Idaho, September 30, 2011.
`
`[PA4] P. J. Hrdlicka and S. Karmakar. Selective targeting of single-stranded DNA using intercalator-
`functionalized oligonucleotides for diagnostic and biotechnological applications. Provisional patent
`application, Univ. Idaho, July 19, 2011.
`
`[PA3] P. J. Hrdlicka, P. Kumar and Michael E. Østergaard. Nucleobase-functionalized conformationally
`restricted nucleotides and oligonucleotides for targeting of nucleic acids. U.S. Patent No. 8,518,908 (issued
`August 2013. Continuation issued on December 2014 as U.S. Patent No. 8,912,318).
`
`[PA2] P. J. Hrdlicka, P. Kumar and Michael E. Østergaard. The use of oligonucleotides modified with
`conformationally restricted C5-functionalized pyrimidine nucleotide building blocks for targeting of nucleic
`acids. Provisional patent application, Univ. Idaho, Sep 4, 2009.
`
`[PA1] P. J. Hrdlicka and P. Kumar, Synthesis and applications of C5-Functionalized Locked Nucleic Acid
`(LNA). Provisional patent application filed, Univ. Idaho, July 31, 2008.
`
`License Agreement:
`Technology for use in diagnostic assays in animal reproduction technology licensed to an undisclosed US
`company. Agreement executed on November 1st 2011.
`
`Published Conference Proceedings/Abstracts:
`
`[CP35] P. J. Hrdlicka. Synthesis and biophysical properties of nucleobase-functionalized LNA (locked
`nucleic acid). 2014 247th American Chemical Society National Meeting (San Francisco, CA), CARB-38.
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`[CP34] P. J. Hrdlicka. Recognition of double-stranded DNA using energetically activated duplexes modified
`intercalator-functionalized nucleotides. 2014 69th Northwest Regional Meeting of the American Chemical
`Society (Missoula, MT), NORM-16.
`
`[CP33] S. Andersen, B. A. Anderson, B. Denn, D. C. Guenther, S. Karmakar, R. L. Rathje, S. P. Sau and P. J.
`Hrdlicka. Invaders: Recognition of double-stranded DNA using energetically activated duplexes modified
`intercalator-functionalized nucleotides. 2014 247th American Chemical Society National Meeting (Dallas,
`TX), CARB-90.
`
`[CP32] M. Kaura, P. Kumar and P. J. Hrdlicka. Synthesis and characterization of oligodeoxyribonucleotides
`modified with nucleobase-functionalized Locked Nucleic Acids (LNAs). 2014 247th American Chemical
`Society National Meeting (Dallas, TX), BIOL-94.
`
`[CP31] S. Karmakar, B. A. Anderson, R. L. Rathje, S. Andersen and P. J. Hrdlicka. High-affinity DNA
`targeting using simplified mimics of N2'-intercalator-functionalized 2'-amino-α-L-LNA. 2012 67th Northwest
`Regional Meeting of the American Chemical Society (Boise, ID), NORM-231.
`
`[CP30] P. J. Hrdlicka. Sequence-unrestricted targeting of double stranded DNA (dsDNA): How to ‘unlock’
`the dsDNA-targeting potential of Invader LNAs. 2012 67th Northwest Regional Meeting of the American
`Chemical Society (Boise, ID), NORM-129.
`
`[CP29] P. J. Hrdlicka. Nucleobase-functionalized Locked Nucleic Acids (LNAs): Optimized probes for
`nucleic acid targeting. 2012 Abstracts of Papers, 243rd ACS National Meeting (San Diego, CA), ORGN-328.
`
`[CP28] P. J. Hrdlicka. Sequence-unrestricted targeting of double stranded DNA (dsDNA): How to ‘unlock’
`the dsDNA-targeting potential of Invader LNAs. 2012 Abstracts of Papers, 243rd ACS National Meeting (San
`Diego, CA), CARB-55.
`
`[CP27] D. C. Guenther, P. Kumar and P. J. Hrdlicka. C5-amino acid functionalized LNA: Synthesis,
`evaluation of biophysical properties, and potential for antisense therapeutics. 2012 Abstracts of Papers, 243rd
`ACS National Meeting (San Diego, CA), BIOL-152.
`
`[CP26] D. C. Julien, A. Giri, M. Papasani, G. Murdoch, P. Hrdlicka and R. A. Hill. Anti-K-Ras siRNA to
`treat pancreatic cancer. Nanotech Conference & Expo 2010: An Interdisciplinary Integrative Forum on
`Nanotechnology, Biotechnology and Microtechnology (Anaheim, CA), 401-404.
`
`[CP25] M. R. Papasani, D. Pokharel, A. Giri, V. V. R. Sai, P. Hrdlicka and R. A. Hill. Oligoethylene glycol
`mediates knockdown effect of small interfering RNAs conjugated goldnanoparticles. Nanotech Conference &
`Expo 2010: An Interdisciplinary Integrative Forum on Nanotechnology, Biotechnology and Microtechnology
`(Anaheim, CA), 358-360.
`
`[CP24] G. Wang, M. R. Papasani, P. J. Hrdlicka and R. A. Hill. Role of serum proteins in the cellular uptake
`of gold-peptide nanoconjugates. Nanotech Conference & Expo 2010: An Interdisciplinary Integrative Forum
`on Nanotechnology, Biotechnology and Microtechnology (Anaheim, CA), 304-307 (featured on Nano
`Science and Technology Institute webpage January 2011).
`
`[CP23] P. Cheguru, M. Ostergaard, M. R. Papasani, V. V. R. Sai, J. Wengel, P. J. Hrdlicka and R. A. Hill.
`Novel nanoprobes to detect mRNA in situ, directed against mouse pyruvate dehydrogenase. Nanotech
`Conference & Expo 2010: An Interdisciplinary Integrative Forum on Nanotechnology, Biotechnology and
`Microtechnology (Anaheim, CA), 300-303.
`
`[CP22] V. V. R. Sai, D. Gangaden, I. Niraula, G. Corti, D. N. McIlroy, D. E. Aston, J. Branen and P. J.
`Hrdlicka. Characterization of Au and Ag nanoparticle coated silica nanosprings - toward SERS based
`diagnostic applications. Nanotech Conference & Expo 2010: An Interdisciplinary Integrative Forum on
`Nanotechnology, Biotechnology and Microtechnology (Anaheim, CA), 19-22.
`
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`HRDLICKA, Patrick J
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`[CP21] S. Gibbon, J.R Branen, M. Frederickson and P. J. Hrdlicka. Identification of important food
`pathogens using LNA (Locked Nucleic Acid) probes. 2010 Joint 65th Northwest and 22nd Rocky Mountain
`Regional Meeting of the American Chemical Society (Pullman, WA), NWRM-207.
`
`[CP20] V. V. R. Sai, D. Gangadean, I. Niraula, G. Corti, D. N. McIlroy, D. E. Aston, J. R. Branen and P. J.
`Hrdlicka. Au and Ag nanoparticle coated silica nanosprings: characterizarion of SERS-active materials and
`detection of DNA from biological threat agents. 2010 Joint 65th Northwest and 22nd Rocky Mountain
`Regional Meeting of the American Chemical Society (Pullman, WA), NWRM-206.
`
`[CP19] B. A. Anderson, S. Karmakar, S. S. Iversen, R. L. Rathje, S. P. Sau and P. J. Hrdlicka. DNA targeting
`using next-generation invader LNAs. 2010 Joint 65th Northwest and 22nd Rocky Mountain Regional Meeting
`of the American Chemical Society (Pullman, WA), NWRM-53.
`
`[CP18] S. P. Sau, S. S. Iversen, R. L. Rathje, B. A. Anderson, S. Karmakar, J. Onley, M. R. Papasani, R. A.
`Hill and P. J. Hrdlicka. Invader LNA - efficient targeting of iso-sequential double stranded DNA. 2010 Joint
`65th Northwest and 22nd Rocky Mountain Regional Meeting of the American Chemical Society (Pullman,
`WA), NWRM-52.
`
`[CP17] M. E. Østergaard, P. Kumar, B. Baral, D. C. Guenther, F. M. Ytreberg and P. J. Hrdlicka. Pyrene-
`functionalized oligonucleotides as probes in nucleic acid diagnostics. 2010 Joint 65th Northwest and 22nd
`Rocky Mountain Regional Meeting of the American Chemical Society (Pullman, WA), NWRM-51.
`
`[CP16] M. E. Østergaard, S. P. Sau, P. Kumar, B. A. Anderson, B. Baral, D. C. Guenther, M. Kaura and P. J.
`Hrdlicka. Optimized nucleic acid targeting using C5-functionalized LNA (Locked Nucleic Acid). 2010 Joint
`65th Northwest and 22nd Rocky Mountain Regional Meeting of the American Chemical Society (Pullman,
`WA), NWRM-50.
`
`[CP15] M. E. Østergaard, B. Baral and P. J. Hrdlicka. Discrimination of single nucleotide polymorphisms
`(SNPs) using brightly fluorescent C5-functionalized Locked Nucleic Acid (LNA) probes. 2010 Abstracts of
`Papers, 239th ACS National Meeting (San Francisco, CA), PHYS-671.
`
`[CP14] M. E. Østergaard, S. P. Sau, P. Kumar, B. A. Anderson, B. Baral, D. C. Guenther and P. J. Hrdlicka.
`Optimized nucleic acid targeting using C5-functionalized LNA (Locked Nucleic Acid). 2010 Abstracts of
`Papers, 239th ACS National Meeting (San Francisco, CA), ORGN-429.
`
`[CP13] S. P. Sau and P. J. Hrdlicka. Invader LNA: Efficient targeting of short double stranded DNA. 2010
`Abstracts of Papers, 239th ACS National Meeting (San Francisco, CA), ORGN-323.
`
`[CP12] B. A. Anderson, R. L. Rathje and P. J. Hrdlicka. DNA targeting using invader nucleic acids. 2010
`Abstracts of Papers, 239th ACS National Meeting (San Francisco, CA), ORGN-305.
`
`[CP11] S. Gibbon, M. E. Østergaard, J.R Branen and P. J. Hrdlicka. Identification of important food
`pathogens using LNA (Locked Nucleic Acid) probes. 2010 Abstracts of Papers, 239th ACS National Meeting
`(San Francisco, CA), AGFD-173.
`
`[CP10] T. S. Kumar, A. S. Madsen, J. Wengel and P. J. Hrdlicka. N2′-Functionalized 2′-amino-alfa-L-LNA:
`A novel class of locked nucleic acids as emerging tools for nucleic acid therapeutics and diagnostics. 2008
`Abstracts of papers, 235th ACS National Meeting (New Orleans, LA), CARB-009.
`
`[CP9] M. E. Østergaard, J. Maity, J. Wengel and P. J. Hrdlicka. 2′-N-(Pyren-1-yl)carbonyl-2′-amino-LNA
`(locked nucleic acid): A versatile label for nucleic acid detection. 2008 Abstracts of papers, 235th ACS
`National Meeting (New Orleans, LA), BIOL-032.
`
`[CP8] N. K. Andersen, J. Wengel and P. J. Hrdlicka. N2′-functionalized 2′-amino--L-LNA adenine
`derivatives - Efficient targeting of single stranded DNA. Nucleosides Nucleotides Nucleic Acids 2007, 26,
`1415-1417.
`
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`[CP7] T. S. Kumar, J. Wengel and P. J. Hrdlicka. Pyrene-functionalized 2′-amino-α-L-LNA as potential
`diagnostic probes. Nucleosides Nucleotides Nucleic Acids 2007, 26, 1407-1409.
`
`[CP6] T. S. Kumar, A. S. Madsen, J. Wengel and P. J. Hrdlicka. Synthesis and biophysical studies of N2′-
`functionalized 2′-amino--L-LNA. Nucleosides Nucleotides Nucleic Acids 2007, 26, 1403-1405.
`
`[CP5] T. Umemoto, P. J. Hrdlicka, B. R. Babu and J. Wengel. Dual-probe system using pyrenylmethyl-
`modified amino-LNA for sensitive SNP genotyping in a homogeneous fluorescence assay. Nucleosides
`Nucleotides Nucleic Acids 2007, 26, 1261-1263.
`
`[CP4] P. J. Hrdlicka, T. S. Kumar and J. Wengel. Synthesis of a 2′-amino--L-LNA-T phosphoramidite.
`Nucleosides Nucleotides Nucleic Acids 2005, 24, 1101-1104.
`
`[CP3] P. J. Hrdlicka, J. S. Jepsen and J. Wengel. Synthesis and biological evaluation of conformationally
`restricted and nucleobase-modified analogs of the anticancer compound 3′-C-ethynylcytidine (ECyd).
`Nucleosides Nucleotides Nucleic Acids 2005, 24, 397-400.
`
`[CP2] B. R. Babu, Raunak, M. D. Sørensen, P. J. Hrdlicka, S Trikha, A. K. Prasad, V. S. Parmar and J.
`Wengel. Novel nucleic acid architectures involving LNA (Locked Nucleic Acid) and pyrene residues –
`Results from an Indo-Danish collaboration. Pure Appl. Chem. 2005, 77, 319-326.
`
`[CP1] P. J. Hrdlicka, B. R. Babu, M. D. Sørensen, N. Harrit and J. Wengel. Ångström-scale chemical
`engineering: Multilabeled 2′-amino-LNA probes for nucleic acid detection in homogenous fluorescence
`assays. In: Collection Symposium Series (M. Hocek, Ed.), 7 (Chemistry of Nucleic Acid Components), 27-28,
`Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 2005.
`
`Published Book Review:
`
`[BR1] P. J. Hrdlicka. ”Modified nucleosides in biochemistry, biotechnology and medicine” from Wiley,
`edited by Piet Herdewijn, ChemBioChem, 2009, 10, 378-379.
`
`Presentations:
`Delivered ~20 invited presentations, ~15 contributed talks and >25 posters at external venues, along with numerous
`internal contributions.
`
`Invited Presentations:
`
`2016: University of Colorado (Denver, CO); University of Southern Denmark (Odense, Denmark); Idaho
`INBRE Research Conference (Moscow, ID).
`
`2015: Alnylam Pharmaceuticals (Cambridge, MA); Gordon Conference on “Nucleosides, Nucleotides and
`Oligonucleotides” (Newport, RI); Alios BioPharma (South San Francisco, CA).
`
`2014: Nucleic Acid Summit 2014 (San Diego, CA); 69th Northwest Regional Meeting of the American
`Chemical Society (Missoula, MT); 248th American Chemical Society Meeting (San Francisco, CA);
`Binghamton University (Binghamton, NY).
`
`2012: 67th Northwest Regional Meeting of the American Chemical Society (Boise, ID); University at Albany
`(Albany, NY).
`
`2011: University of Aarhus (Aarhus, Denmark); Carnegie Mellon University (Pittsburgh, PA); University of
`Copenhagen (Copenhagen, Denmark); Nucleic Acid Center Mini-symposium on “Nucleic Acid Chemical
`Biology" (Odense, Denmark).
`
`2010: ISIS Pharmaceuticals (Carlsbad, CA); Minitube of America (Mt. Horeb, WI); Washington State
`University (Pullman, WA).
`
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`2008: University Southern Denmark (Odense, Denmark).
`
`2007: Washington State University (Pullman, WA); Gordon Conference on “Nucleosides, Nucleotides and
`Oligonucleotides” (Newport, RI).
`
`Contributed Talks:
`
`2017: Washington State University, School of Molecular Bioscience.
`
`2016: Eastern Washington University; University of Alaska, Fairbanks.
`
`2014: 247th American Chemical Society National Meeting (Dallas, TX); Weber State University; Utah State
`University; Utah Valley University; Central Washington University; Brigham Young University (main
`campus); University of Utah; Brigham Young University (Idaho campus); Idaho State University.
`
`2013: University of Montana; Eastern Washington University; Eastern Oregon University.
`
`2012: 243th American Chemical Society National Meeting (San Diego, CA) – two presentations.
`
`2010: 65th Northwest / 22nd Rocky Mountain Regional Meeting of the American Chemical Society (Pullman,
`WA); 239th American Chemical Society Conference (San Francisco, CA).
`
`2008: 235th American Chemical Society National Meeting (New Orleans, LA).
`
`2007: AAAS Pacific Division, 88th Annual Meeting of the Pacific Division Meeting & 62nd Annual Meeting
`of the Northwest Region, American Chemical Society (Boise, ID); Gonzaga University.
`
`Student Presentations:
`
`2016: Idaho INBRE Research Conference (Moscow, ID) - student presented a poster.
`
`2015: Idaho INBRE Research Conference (Moscow, ID) - student presented a poster.
`
`2014: 10th Annual Oligonucleotide Therapeutics Society Meeting (San Diego, CA) – student presented poster
`and received the 2014 Dr. Alan