Journal Articles

Sergio Barberán-Soler* , Jenny M. Vo, Ryan E. Hogans, Anne Dallas, Brian H. Johnston and Sergei A. Kazakov* (2018)  Decreasing miRNA sequencing bias using a single adapter and circularization approach. Genome Biology, 19:105 Download PDF

Dallas A, Trotsyuk A, Ilves H, Bonham CA, Rodrigues M, Engel K, Barrera JA, Kosaric N, Stern-Buchbinder ZA, White A, Mandell KJ, Hammond P, Mansbridge JN, Jayasena S, Gurtner GC, Johnston BH (2018) Acceleration of Diabetic Wound Healing with PHD2- and miR-210-targeting Oligonucleotides. Tissue Eng Part A 2018 Jun 29  Download PDF

A.Dallas, H. Ilves, H. Ma, D. J. Chin, I. MacLachlan, K. Klumpp, and B.H. Johnston (2014) Inhibition of hepatitis C virus in chimeric mice by sshRNAs:  sequence analysis of surviving virus shows added selective pressure of combination therapy. J. Virology May;88(9):4647-56. PMID: 24478422  Download PDF

Ma H. , Dallas A, Ilves H,Shorenstein J, Maclachlan I, Klumpp K, and Johnston BH (2014) Formulated minimal-length synthetic shRNAs are potent inhibitors of Hepatitis C virus in chimeric human-liver mice.  Gastroenterology, 146(1):63-66.e5. PMID: 24076507   Download PDF

A. Dallas and B.H. Johnston (2013) Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers.  In: siRNA Design, D. J. Taxman, ed., Methods in Molecular Biology series, Humana Press (Springer), New York.  PMID: 23027057   Download PDF

Dallas A, Ilves H, Shorenstein J, Judge A, Spitler R, Contag C, Ping Wong S, Harbottle RP, MacLachlan I, and Johnston BH (2013) Minimal-length synthetic shRNAs (sshRNAs) formulated with lipid nanoparticles are potent inhibitors of hepatitis C virus IRES-linked gene expression in mice.  Mol. Therapy–Nucleic Acids 17;2:e123. PMID: 24045712   Download PDF

Kolli S, Wong SP, Harbottle R, Johnston B, Thanou M, Miller AD. (2013) pH-Triggered Nanoparticle Mediated Delivery of siRNA to Liver Cells in Vitro and in Vivo. Bioconjug Chem. 24(3):314-32. PMID: 23305315   Download PDF

B.H. Johnston and Q. Ge (2012) Design of synthetic shRNAs for targeting hepatitis C: A new approach to antiviral therapeutics.  In: RNA Technologies, From Nucleic Acids Sequences to Molecular Medicine, V. A. Erdmann and J. Barciszewski, Eds., Springer, Berlin. DOI 10.1007/978-3-642-27426-8_18.  Download PDF

Dallas A, Ilves H, Ge Q, Kumar P, Shorenstein J, Kazakov SA, Cuellar TL, McManus MT, Behlke MA, Johnston B (2012) Right- and Left-loop short shRNAs have distinct and unusual mechanisms of gene silencing. Nucleic Acids Res. 40: 9255–9271. PMID: 22810205   Download PDF

Li F, Pignatta D, Bendix C,  Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B (2012) MicroRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. USA 109(5):1790-5 PMID: 22307647   Download PDF

Kumar P, Johnston BH, Kazakov SA (2011) miR-ID: a novel, circularization-based platform for detection of microRNAs. RNA 17(2):365-80 PMID 21169480  Download PDF

Ge Q, Ilves H, Dallas A, Kumar P, Shorenstein J, Kazakov SA, and Johnston BH (2010) Minimal-length short hairpin RNAs: The relationship of structure and RNAi activity. RNA 16(1):106-17 PMID 19952116  Download PDF

Ge Q, Dallas A, Ilves H, Shorenstein J, Behlke MA, Johnston BH (2010) Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. RNA 16(1):118-30 PMID 19948766   Download PDF

Dallas A, Balatskaya SV, Kuo T-C, Vlassov AV, Kaspar RL, Kisich K, Kazakov SA, Johnston BH (2008) Hairpin ribozyme-antisense RNA derivatives act as molecular Lassos. Nucleic Acids Res. 36(21):6752-66; PMID 18953032   Download PDF

Hickerson RP, Vlassov AV,  Wang Q,  Leake D, Ilves H,  Contag CH, Johnston BHKaspar RL (2008) Stability study of unmodified siRNA and relevance to clinical use.  Oligonucleotides 18(4):345-54; PMID 18844576   Download PDF

Seyhan AA, Alizadeh BN, Johnston BH (2007) RNA interference-mediated inhibition of Semliki Forest virus replication in mammalian cells.  Oligonucleotides 17(4): 473-84. PMID 18095875   Download PDF

Wang Q,  Ilves H,  Chu P,  Contag CH,  Leake D, Johnston BH, Kaspar RL (2007)  Delivery and inhibition of reporter genes by small interfering and hairpin RNAs in a mouse skin model. J. Invest. Dermatol. 127(11):2577-84;  PMID 17522708   Download PDF

Vlassov AV, Korba B, Farrar K, Mukerjee S, Seyhan AA, Ilves H, Kaspar RL, Kazakov SA, Johnston BH (2007) shRNAs targeting hepatitis C: effects of sequence and structural features, and comparison with siRNA. Oligonucleotides 17:223-236. PMID 17638526   Download PDF

Ilves H, Kaspar RL, Wang Q, Seyhan AA, Vlassov AV, Contag CH, Leake D, Johnston BH (2006) Inhibition of hepatitis C IRES-mediated gene expression by small hairpin RNAs in human hepatocytes and mice. Ann. N.Y. Acad. Sci., 1082: 52-55. PMID 17145925   Download PDF

Seyhan AA, Vlassov AV, Johnston BH (2006) RNA interference from multimeric shRNAs generated by rolling circle transcription.  Oligonucleotides 16: 353-363. PMID 17155910   Download PDF

Kazakov SA, Balatskaya SV, Johnston BH (2006)  Ligation of the hairpin ribozyme in cis induced by freezing and dehydration. RNA 12: 446-456. PMID 16495237   Download PDF

Vlassov AV, Johnston BH, and Kazakov SA (2005) Hairpin ribozyme-catalyzed ligation in water-alcohol solutions.  Oligonucleotides 15, 303-309. PMID 16396624   Download PDF

Wang Q, Contag CH, Ilves H, Johnston BH, Kaspar RL (2005) Small hairpin RNAs efficiently inhibit hepatitis C IRES-mediated gene expression in human tissue culture cells and a mouse model. Mol. Therapy, 12:562-8. PMID 15953767   Download PDF

Vlassov AV, Kazakov SA, Johnston BH, Landweber LF (2005) The RNA World on Ice: A New Scenario for the Emergence of RNA Information, J. Mol. Evol., 61:264-73. PMID 16044244   Download PDF

Seyhan AA, Vlassov AV, Ilves H, Egry L, Kazakov SAJohnston BH (2005) Complete, gene-specific siRNA libraries: production and expression in mammalian cells. RNA 11, 837-846. PMID 15840823  Download PDF

Vlassov AV, Koval OA, Johnston BH, Kazakov SA (2004) ROLL: a method of preparation of gene-specific oligonucleotide libraries. Oligonucleotides 14, 210-220. PMID 15625916  Download PDF

Vlassov, AV, Johnston, BH and Kazakov, SA (2004) Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucl. Acids Res. 32, 2966-2974. PMID 15161960  Download PDF

Book Chapters

Dallas A, Johnston, BH (2013) Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers.  In: siRNA Design: Methods and Protocols, Methods in Molecular Biology, vol. 942, 279-290   Download PDF

Kazakov, SA, Johnston, BH (2009)  Development of Gene-Profile-Responsive Antisense Agents.  In: Gene Profiles in Drug Design, CRC Press, 29-56   Download PDF

Dallas A, Vlassov AV, Kazakov SA (2004) Principles of Nucleic Acid Cleavage by Metal Ions. In: Nucleic Acids and Molecular Biology, Vol. 13, 61-88   Download PDF