Olfaction Biochemistry

“Conformational sensing by a mammalian olfactory receptor,” M.T. Liu, M. Na, Y. Li, M. Biscoe, and K. Ryan*, Chemistry-A European Journal, 2020, Vol. 26(50), pp 11345-11655 (September 4, 2020 issue) https://doi.org/10.1002/chem.202001390 or https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202003590

“Single-neuron comparison of the olfactory receptor response to deuterated and non-deuterated odorants,” Mihwa Na, Min Ting Liu, Minh Q. Nguyen and Kevin Ryan*, ACS Chemical Neuroscience. 2019, 10, 1, 552-562 DOI: 10.1021/acschemneuro.8b00416, Published online Oct. 22, 2018.

“Carbon chain shape selectivity by the mouse olfactory receptor OR-I7,” Min Ting Liu,Jianghai Ho, Jason Liu, Radhanath Purakait, Uriel N. Morzan, Lucky Ahmed, Victor S. Batista, Hiroaki Matsunami,* and Kevin Ryan* Organic and Biomolecular Chemistry, 2018, 16, 2541-2548. PMCID: PMC6067823. https://doi.org/10.1039/C8OB00205C

“Aldehyde Recognition and Discrimination by Mammalian Odorant Receptors via Functional Group-Specific Hydration Chemistry,” Li Y, Peterlin Z, Ho J, Yarnitzky T, Liu MT, Fichman M, Niv MY, Matsunami H, Firestein S,* Ryan K.* ACS Chemical Biology. (2014) Vol. 9 (11): 2563-71; PMID: 25181321; PMCID: PMC4245160. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245160/

“Discrimination of saturated aldehydes by the rat I7 olfactory receptor,” M.D. Kurland, M.B. Newcomer, Z. Peterlin, K. Ryan, S. Firestein, and V.S. Batista*, Biochemistry, 2010, 3, 49(30):6302-4. PMCID: PMC2912408

“Molecular Shape and the Sense of Smell,” Kevin Ryan* and Xiaozhou P. Ryan, book chapter in The 2010 McGraw-Hill Yearbook of Science and Technology, 2010, 243-245.

“The Importance of Odorant Conformation to the Binding and Activation of a Representative Olfactory Receptor,” Zita Peterlin, Yadi Li, Grant Sun, Rohan Shah, Stuart Firestein, and Kevin Ryan* Cell Chemical Biology (formerly Chemistry & Biology), 2008 15, 12, 1317-1327. https://pubmed.ncbi.nlm.nih.gov/19101476/

Small RNA Expression Vectors

Starting and Stopping RNA Polymerase III Transcription on Single-stranded DNA Oligonucleotides Lama, L. and Ryan, K.* RNA. Oct 2022; 28 (10) (epub July 2022). doi:10.1261/rna.078981.121

“Starting and Stopping RNA Polymerase III Transcription on Single-stranded DNA Oligonucleotides,” Lodoe Lama and Kevin Ryan*(under peer review). https://pubmed.ncbi.nlm.nih.gov/27593562/

Small RNA-seq: The RNA 5’ end ligation problem and a method to circumvent it,” L. Lama, J. Cobo, D. Buenaventura and K. Ryan,* Journal of Biological Methods 2019, Vol. 6(1) e108,  DOI: 10.14440/jbm.2019.269. https://doi.org/10.14440/jbm.2019.269

“RNA polymerase III initiation on coligo DNA templates containing loops of variable sequence, size and nucleotide chemistry,” Joy Patel, Lodoe Lama, Niklas Hoffmann, Jose Cobo Christoph Müller and Kevin Ryan,* Gene (2016) 612:49-54 Epub September 2, 2016, http://dx.doi.org/10.1016/j.gene.2016.09.001

“Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I,” Lodoe Lama and Kevin Ryan,* RNA 2016 Jan; 22(1):155-61. DOI: 10.1261/rna.054999.115. Epub 2015 Nov 13. PMID: 26567315; PMCID: PMC4691829 https://pubmed.ncbi.nlm.nih.gov/26567315/

“New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III,” Lodoe Lama, Christine I. Seidl and Kevin Ryan,* 2014 Transcription, Vol. 5, Issue 2. Published online 27 January 2014; http://dx.doi.org/10.4161/trns.27913; PMID: 24531370 OR https://pubmed.ncbi.nlm.nih.gov/25764216/

“Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells,” C.I. Seidl, L. Lama and K. Ryan*, 2012 Nucleic Acids Research 2013 41 (4): 2552-2564. doi: 10.1093/nar/gks1334 First published online: December 28, 2012. PMCID: PMC3575851 https://pubmed.ncbi.nlm.nih.gov/23275570/

“Circular Single-Stranded Synthetic DNA Delivery Vectors for microRNA,” C. Seidl and K. Ryan*, PLoS One, Feb. 2011 6(2): e16925. doi:10.1371/journal.pone.0016925. PMCID: PMC3040211 https://pubmed.ncbi.nlm.nih.gov/21359172/

“Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases,” Dongyu Liu, Sarah L. Daubendiek, Martin A. Zillman, Kevin Ryan, and Eric T. Kool,* Journal of the American Chemical Society, 1996, 118, 1587-94. https://pubmed.ncbi.nlm.nih.gov/20830216/

“Rolling-Circle RNA Synthesis: Circular Oligonucleotides as Efficient Substrates for T7 RNA Polymerase,” Sarah L. Daubendiek, Kevin Ryan, and Eric T. Kool,* Journal of the American Chemical Society, 1995, 117, 7818-7819. https://pubmed.ncbi.nlm.nih.gov/27524830/

pre-mRNA Processing

“Optimizing In Vitro Pre-mRNA 3′ Cleavage Efficiency: Reconstitution from Anion-Exchange Separated HeLa Cleavage Factors and from Adherent HeLa Cell Nuclear Extract,” Na, M., Valente, S. and Ryan, K.*Methods in Molecular Biology (2017) Eukaryotic Transcription and Post-Transcription Gene Expression Regulation Vol. 1507, Chapter 14 (Springer Publishing ISBN 978-1-4939-6516-8) November 2016 https://link.springer.com/protocol/10.1007%2F978-1-4939-6518-2_14

“An investigation into the role of ATP in the mammalian pre-mRNA 3’ cleavage reaction,” Khleborodova, A., Nagre, N., Pan, X., and Ryan, K.* Biochimie 2016 (April 6) 125: 213-222. PMID 27060432; PMCID not yet available. DOI: 10.1016/j.biochi.2016.04.004 OR https://pubmed.ncbi.nlm.nih.gov/27060432/

“Analysis of RNA processing reactions using cell free systems: 3′ end cleavage of pre-mRNA substrates in vitro,” Joseph Jablonski, Mark Clementz, Kevin Ryan and Susana T. Valente,* J Vis Exp. (JoVE), 2014 May 3, (87). doi: 10.3791/51309. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030693/

“Structurally diverse low molecular weight activators of the mammalian pre-mRNA 3’ cleavage reaction,” Min Ting Liu, Nagaraja N. Nagre, and Kevin Ryan,* Bioorganic and Medicinal Chemistry 2013 Jan 15; 22(2):834-41. doi: 10.1016/j.bmc.2013.12.006. Published online 2013 Dec. 15. PMID: 24373842 https://doi.org/10.1016/j.bmc.2013.12.006

“Small-molecule activators of pre-mRNA 3’ cleavage,” Kevin Ryan*, Asya Khleborodova, Jingyi Pan, and Xiaozhou P. Ryan RNA, 2009 15, 3, 483-492. PMCID: PMC2657006 https://pubmed.ncbi.nlm.nih.gov/19155323/

“Finishing Touches: Post-Translational Modification of Protein Factors Involved in Mammalian pre-mRNA 3’ End Formation,” Kevin Ryan* and David L.V. Bauer, Int. J. Biochem. & Cell Bio. 2008 40, 11,2384-2396. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2548416/

“Pre-mRNA 3’ Cleavage is Reversibly Inhibited in Vitro by Cleavage Factor Dephosphorylation,” Kevin Ryan*, RNA Biology, 2007, 4 (1) 26-33. https://pubmed.ncbi.nlm.nih.gov/17585202/

“Symplekin and xGLD-2 are required for CPEB-mediated cytoplasmic polyadenylation,” Daron Barnard, Kevin Ryan, James L. Manley and Joel Richter*, Cell, 2004, 119 (5), 641-51. https://pubmed.ncbi.nlm.nih.gov/15550246/

“Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease,” Kevin Ryan, Olga C. Calvo and James L. Manley*, RNA, 2004, 10 (4):565-73. https://pubmed.ncbi.nlm.nih.gov/15037765/

“Requirements of the RNA Polymerase II C-Terminal Domain for Reconstituting pre-mRNA Cleavage,” Kevin Ryan, Kanneganti G.K. Murthy, Syuzo Kaneko and James L. Manley*, Molecular and Cellular Biology, 2002, 22, 6, 1684-1692. https://pubmed.ncbi.nlm.nih.gov/11865048/

“Phosphorylation of CPEB by Eg2 Mediates the Recruitment of CPSF into an Active Cytoplasmic Polyadenylation Complex,” Raul Mendez, Kanneganti G.K. Murthy, Kevin Ryan, James L. Manley and Joel D. Richter,* Molecular Cell, 2000, Nov; 6(5):1253-9. https://pubmed.ncbi.nlm.nih.gov/11106762/

Medicinal Chemistry

“A Synthetic Receptor Motif Designed for Extended Peptide Conformations” Kevin Ryan, Leland Gershell, and W. Clark Still,* Tetrahedron, 2000, 21, 3309-3318. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557054/

“Inhibition of Gene Expression in Human Cells Through Small Molecule-RNA Interactions” Seongwoo Hwang, Natarajan Tamilarasu, Kevin Ryan, Ikramul Huq, W. Clark Still, and Tariq M. Rana,* Proceedings of the National Academy of Sciences, USA, 1999, 96, 23, 12997-13002. https://doi.org/10.1073/pnas.96.23.12997

“Construction of Sequence-Selective Peptide Receptors from Conformationally Restricted Eta– and Theta– Amino Acids,” Kevin Ryan and W. Clark Still,* Bioorganic and Medicinal Chemistry Letters, 1999, 9, 2673-2678. https://pubmed.ncbi.nlm.nih.gov/10509914/

“Triplex-Directed Self-Assembly of an Artificial Sliding Clamp on Duplex DNA,” Kevin Ryan and Eric T. Kool,* Cell Chemical Biology (formerly Chemistry & Biology), 1998, 5:59-67.  Also featured on the cover of this issue. https://www.sciencedirect.com/science/article/pii/S1074552198901405

“Synthesis and Reactivity of Pyrrolo[3,2,E]indole: Removal of an N-bom Group From an Unactivated Indole,” John E. Macor,* James T. Forman, Ronald J. Post and Kevin Ryan, Tetrahedron Letters, 1997, 38, 10, 1673-1676. https://www.sciencedirect.com/science/article/abs/pii/S0040403997001986

“A Direct Synthesis of 3-(Pyrrolidin-3-yl)indoles for Use As Conformationally Restricted Analogs of Tryptamines” John E. Macor, David H. Blank, Kevin Ryan, Ronald J. Post, Synthesis 1997, 443-449. https://www.thieme-connect.com/products/ejournals/abstract/10.1055/s-1997-1214

“5-(3-Nitropyrid-2-ylamino)indoles: Novel Serotonin Agonists with Selectivity for the 5-HT1D Receptor. Variation at C3 of the Indole Template Leads to Increased 5-HT1D Receptor Selectivity,” John E. Macor,* David H. Blank, Carol B. Fox, Lorraine A. Lebel, Michael E. Newman, Kevin Ryan, Ronald J. Post, Anne W. Schmidt, David W. Shullz, and B. Kenneth Koe, Journal of Medicinal Chemistry, 1994, 37, 2509. https://pubmed.ncbi.nlm.nih.gov/8057297/

“The Synthesis of a Conformationally Restricted Analog of the Neurotransmitter Serotonin with Reduced Basicity,” John E. Macor and Kevin Ryan, Heterocycles, 1994, 37, 1447. DOI: 10.3987/COM-93-S71

“A Simple Synthesis of 5-Amino-3-(2-dimethylaminoethyl) indole[5-amino-N,N-dimethyl-tryptamine],” John E.Macor,* Ronald J.Post, and Kevin Ryan, Synthetic Communications, 1993, 23, 65. https://www.tandfonline.com/doi/abs/10.1080/00397919308020402

“Synthesis and Serotonergic Pharmacology of the Enantiomers of 3-[(N-Methylpyrrolidin-2-yl)methyl]-5-methoxy-1H-indole: Discovery of Stereogenic Differentiation in the Aminoethyl Side Chain of the Neurotransmitter Serotonin,” John E. Macor ,* James Blake, Carol B. Fox, Celeste Johnson, B. Kenneth Koe, Lorraine A. Lebel, Jean M. Morrone, Kevin Ryan, Anne W. Schmidt, David W. Schulz, and Stevin H. Zorn, Journal of Medicinal Chemistry,1992, 35, 4503-4505. https://pubmed.ncbi.nlm.nih.gov/1447752/

“A Synthesis of 5-Carboxamidopyrrolo[3,2-b]pyridine,” John E. Macor*, Ronald Post and Kevin Ryan, Journal of Heterocyclic Chemistry, 1992, 29, 1465-1467. https://onlinelibrary.wiley.com/doi/10.1002/chin.199317182

“Synthesis of a Conformationally Restricted Analog of the Anti-Migraine Drug Sumatriptan,” John E. Macor,* David H. Blank, Ronald J.Post and Kevin Ryan, Tetrahedron Letters, 1992, 33, 52, 8011-8014 . https://doi.org/10.1016/S0040-4039(00)74703-4

“The Synthesis of Pyrano[3,2-e]indoles and Pyrano[2,3-f]indoles as Rotationally Restricted Phenolic Analogs of the Neurotransmitter Serotonin,” John E. Macor*, Kevin Ryan, and Michael E. Newman, Tetrahedron, 1992, 48, 6, 1039-1052. https://www.sciencedirect.com/science/article/abs/pii/S0040402001882004

“Synthesis of Some Conformationally Restricted Serotonin Analogs,” John E. Macor* and Kevin Ryan, Heterocycles, 1990, 31, 8, 1497-1504 DOI: 10.3987/COM-90-5434

“Synthesis of [3H]CP-93,129: A  Radioligand Selective for the 5-HT1B Receptor,” John E. Macor,* Kevin Ryan, Phillip M. Chalabi, James C. Windels, and Robert W. Roth, Journal of Labelled Compounds and Radiopharmaceuticals, 1990 Vol.XXVIII, No.11, 1293. https://doi.org/10.1002/jlcr.2580281109

“3-(1,2,5,6-Tetrahydropyrid-4-yl)pyrrolo[3,2-b]pyrid-5-one: A Potent and Selective Serotonin (5HT1B) Agonist and Rotationally Restricted Phenolic Analog of 5-Methoxy-3-(1,2,5,6-tetrahydropyrid-4-yl)indole,” John E. Macor,* Carol A. Burkhart, James H. Heym, Jeffrey L. Ives, Lorraine A. Lebel, Michael E. Newman, Jann A. Nielsen, Kevin Ryan, David W. Schulz, Leslie K. Torgersen, and B. Kenneth Koe, Journal of Medicinal Chemistry, 1990, 33, 2087-2093. https://pubmed.ncbi.nlm.nih.gov/2374139/

“Synthesis of Pyrano[4,3-b]indoles as Conformationally Restricted Analogues of the Serotonin Antagonist ICS 205-930 and as Precursors to 2-Vinylindoles,” John E. Macor,* Kevin Ryan, and Michael E. Newman, Journal of Organic Chemistry, 1989, 54, 20, 4785-4795. https://pubs.acs.org/doi/abs/10.1021/jo00281a018

“A Simple Synthesis of 2-Vinylindoles,” John E. Macor,* Kevin Ryan and Michael E. Newman, Tetrahedron Letters,1989,30, 19, 2509-2512. DOI:10.1016/s0040-4039(01)80437-8