University of Idaho

Coauthored 37 peer-reviewed articles and reviews (cited >600 times in >300 different publications; H-index = 14); seven patent applications; two book chapters; >30 published conference proceedings/abstracts; one published book review. For a complete publication list, click here.

[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.

[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.

[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 DNA/RNA hybridization probes", J. Org. Chem., 2012, 77, 5-16.

[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] Michael E. Østergaard and Patrick 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.

[30] 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.

[29] 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.

[28] V. V. R. Sai, D. Gangadean, I. Niraula, G. Corti, D. N. McIlroy, D. E. Aston, J. R. Branen, and P. J. Hrdlicka, “Characterization of Au- and Ag-nanoparticle coated silica nanosprings – Toward SERS based diagnostic applications”, 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: Unpalleled 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, 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, P. J. Hrdlicka. “Selective Deacylation of Peracylated Ribonucleosides”, Tetrahedron Lett., 2009, 50, 1751-1753.

[16] T. S. Kumar, A. S. Madsen, M. E. Østergaard, S. P. Sau, J. Wengel and P. J. Hrdlicka, ”Functionalized 2′-Amino-a-L-LNA - Directed Positioning of Intercalators for DNA Targeting”, J. Org. Chem. 2009, 74, 1070-1081.

[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.

[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-alpha-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-alpha-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 a-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-alpha-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.

[6] P. J. Hrdlicka, T. S. Kumar and J. Wengel, “Targeting of Mixed Sequence Double-Stranded DNA Using Pyrene-Functionalized 2’-Amino-alpha-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 Signalling of Full Complementarity”, Chem. Commun. 2004, 1478–1479.

[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.