67. Dual roles of fucoidan-GPIba interaction in thrombosis and hemostasis: implications for drug development targeting GPIba. Shen, C., Mackeigan, D.T., Shoara, A.A., Xu, R., Bhoria, P., Karakas, D., Ma, W., Cerenzia, E., Chen, Z.Y., Hoard, B., Lin, L., Lei, X., Zhu, G., Chen, P., Johnson, P.E., Ni, H., (2023) Journal of Thrombosis and Haemostasis, in press.
66. The search for the lost dissociation constant of electrochemical aptamer-based biosensors. Rahbarimehr, E., Chao, H.P., Churcher, Z.R, Slavkovic, S., Kaiyum, Y.A., Johnson, P.E. and Dauphin-Ducharme, P. (2023) Analytical Chemistry, in press.
65. Tuning the DNA binding properties of phenolic hemicyanine dyes for host-guest fluorescent aptasensor applications. Van Riesen, A.J., Kalnitsky,B., Shoara, A.A., Slavkovic, S., Churcher, Z.R, Johnson, P.E. and Manderville, R.A. (2023) Dyes and Pigments, 209, 110936
64. Analysis of Aptamer-Small Molecule Binding Interactions Using Isothermal Titration Calorimetry. Slavkovic, S. and Johnson, P.E. (2023) in Nucleic Acid Aptamers: Selection, Characterization, and Application, 2nd edition, vol 2570. (editors: Mayer G. and Menger M.M.) as part of the series Methods in Molecular Biology. Humana: New York, NY, pp 105-118.
63. Fluorometry Studies of Aptamers That Bind Intrinsically Fluorescent Ligands: Techniques, Obstacles and Optimizations. Shoara, A.A. and Johnson, P.E. (2022) Aptamers, 6, in press.
62. The minimum aptamer publication standards (MAPS guidelines) for de novo aptamer selection. McKeague, M., Calzada, V., Cerchia, L., DeRosa, M., Heemstra, J.M., Janic, N., Johnson, P.E., Kraus, L., Limson, J., Mayer, G., Nilsen-Hamilton, M., Porciani, D., Sharma, T.K., Suess, B., Tanner, J.A., Shigdar, S. (2022) Aptamers, 6, 10-18.
61. DNA Binding by the Antimalarial Compound Artemisinin. Slavkovic, S., Shoara, A.A., Churcher, Z.R, Daems, E., de Wael, K., Sobott, F., and Johnson, P.E. (2022) Scientific Reports, 12, 133.
60. Cooperative binding by a bifunctional deoxycholic acid and cocaine-binding aptamer. Dawood, N., Slavkovic, S., Qureshi, R., Khamissi, N., Bauer, C., Reinstein, O. and Johnson, P.E. (2021) Aptamers, 5, 31-38.
59. Weak Binding of Levamisole by the Cocaine-Binding Aptamer Does Not Interfere with an Aptamer-based Detection Assay. Shoara, A.A., Churcher, Z.R., Slavkovic, S. and Johnson, P.E. (2021) ACS Omega, 6, 24209-24217.
58. A Visible Fluorescent Light-up Probe for DNA Three-Way Junctions Provides Host-Guest Biosensing Applications. Van Riesen, A.J., Le, J., Slavkovic, S., Churcher, Z.R, Shoara, A.A., Johnson, P.E. and Manderville, R.A. (2021) ACS Applied Bio Materials, 4, 6732-6741.
57. How to Develop and Prove High-Efficiency Selection of Ligands from Oligonucleotide Libraries: A Universal Framework for Aptamers and DNA-Encoded Small-Molecule Ligands. Le, A.T.H., Krylova, S.M., Beloborodov, S.S., Wang, T.Y., Hili, R., Johnson, P.E., Li, F., Veedu, R.N., and Krylov, S.N. (2021) Analytical Chemistry, 93, 5343-5354.
56. HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain. Kwan, J.J., Slavkovic, S., Piazza, M., Wang, D., Dieckmann, T., Johnson, P.E., Wen, X.-Y. and Donaldson, L.W. (2020) Commun Biol, 3, 672.
55. Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism. Slavkovic, S. Zhu, Y., Churcher, Z.R., Shoara, A.A., Johnson, A.E. and Johnson, P.E. (2020) Scientific Reports, 10, 18944.
54. NMR for non-experts; a practical guide for applying NMR methods in studies of aptamer-ligand interactions. Churcher, Z.R., and Johnson, P.E. (2020) Aptamers, 4, 3-9. link
53. Reduction in Dynamics of Base Pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer. Churcher, Z.R., Garaev, D.M., Hunter, H.N. and Johnson, P.E. (2020) Biophysical Journal, 119, 1147-1156.Â
52. Analysis of the Role Played by Ligand-Induced Folding of the Cocaine-Binding Aptamer in the Photochrome Aptamer Switch Assay. Shoara, A.A., Churcher, Z.R., Steele, T.W.J. and Johnson, P.E. (2020) Talanta, 121022.
51. Designed Alteration of Binding Affinity in Structure-Switching Aptamers Through the Use of Dangling Nucleotides. Slavkovic, S., Eisen, S.R. and Johnson, P.E. (2020) Biochemistry, 59, 663-670.
50. A unique conformational distortion mechanism drives Lipocalin 2 binding to bacterial siderophores. Huang, X., Slavkovic, S., Song, E., Botta, A., Mehrazma, B., Lento, C., Johnson, P.E., Sweeney, G. and Wilson, D.J. (2020) ACS Chemical Biology, 15, 234-242.
49. Aptamers 2019 - A conference update. Shigdar, S., Johnson, P.E., Pietruschka, G., Legen, T., Mayer, G. and McKeague, M. (2019) Aptamers, 3, 1-3.
48. A proof of concept application of aptachain: ligand-induced self-assembly of a DNA aptamer. Neves, M.A.D., Slavkovic, S., Reinstein, O., Shoara, A.A., and Johnson, P.E. (2019) RSC Advances, 9, 1690-1695.
47. Nanomolar Binding Affinity of Quinine-Based Antimalarial Compounds by the Cocaine-Binding Aptamer. Slavkovic, S., Churcher, Z.R. and Johnson, P.E. (2018) Bioorganic & Medicinal Chemistry, 26, 5427-5434.
46. Aptamers 2018 - A conference update. Tanner, J.A., Ismail, S.I., Shigdar, S., DeRosa M.C., Hahn, U., Johnson, P.E., Suess, B. and McKeague, M. (2018) Aptamers, 2, 52-54.
45. Isothermal titration calorimetry studies of aptamer-small molecule interactions: practicalities and pitfalls. Slavkovic, S. and Johnson, P.E. (2018) Aptamers, 2, 45-51.
44. Aptamers 2017 at Oxford. Henri, J., McKeague, M., Johnson, P.E., Suess, B., Nakamura, Y., Nilsen-Hamilton, M., Pastor, F., Hahn, U., Bunka, D. and Shigdar, S. (2018) Aptamers, 2, 11-14.
43. Development of a thermal-stable structure-switching cocaine-binding aptamer. Shoara, A.A., Reinstein, O., Borhani, O.A., Martin, T.R., Slavkovic, S., Churcher, Z.R. and Johnson, P.E. (2018) Biochimie, 145, 137-144.
42. Aptamer facilitated purification of functional proteins. Beloborodov, S.S., Bao, J., Krylova, S.M., Shala-Lawrence, A., Johnson, P.E. and Krylov, S.N. (2018) J. Chromatography B., 1073, 201-206.
41. Optimizing stem length to improve ligand selectivity in a structure-switching cocaine-binding aptamer. Neves, M.A.D., Shoara, A.A., Reinstein, O., Borhani, O.A., Martin, T.R. and Johnson, P.E. (2017) ACS Sensors, 2, 1539-1545
40. Analysis of the Interaction between the Cocaine-Binding Aptamer and its Ligands using Fluorescence Spectroscopy. Shoara, A.A., Slavkovic, S., Donaldson, L.W. and Johnson, P.E. (2017) Can. J. Chem. 95, 1253-1260.
39. Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions. Harkness V, R.W., Johnson P.E. and Mittermaier, A.K. (2017) J. Visualized Exp. (129) e55959
38. Comparison of the Free and Ligand-Bound Imino Hydrogen Exchange Rates for the Cocaine-Binding Aptamer. Churcher, Z.R., Neves, M.A.D., Hunter, H.N. and Johnson P.E. (2017) Journal of Biomolecular NMR, 68, 33-39. or
37. Salt-Mediated Two-Site Binding by the Cocaine-Binding Aptamer. Neves, M.A.D., Slavkovic, S., Churcher, Z.R. and Johnson P.E. (2017) Nucleic Acids Research, 45, 1041-1048
36. Rapid Characterization of Folding and Binding Interactions with Thermolabile Ligands by DSC. Harkness V, R.W., Slavkovic, S., Johnson P.E. and Mittermaier, A.K. (2016) Chemical Communications, 52, 13471-13474
35. Colorimetric Detection of Catalase and Catalase-Positive Bacteria (E. coli) Using Silver Nanoprisms. Zhao, L., Wiebe, J., Zahoor, R., Slavkovic, S., Malile, B., Johnson P.E. and Chen J.I.L. (2016) Analytical Methods, 8, 6625-6630
34. Structure-Affinity Relationship of the Cocaine-Binding Aptamer with Quinine Derivatives. Slavkovic, S., Altunisik, M., Reinstein, O. and Johnson, P.E. (2015) Bioorganic & Medicinal Chemistry, 23, 2593-2597
33. Pre-equilibration kinetic size-exclusion chromatography with mass spectrometry detection (peKSEC-MS) for label-free solution-based kinetic analysis of protein-small molecule interactions. Bao, J., Krylova, S.M., Cherney, L.T., Le Blanc, J.C.Y., Pribil, P., Johnson, P.E., Wilson, D.J., and Krylov, S.N. (2015) Analyst, 140, 990-994.
32. Kinetic Size-Exclusion Chromatography with Mass Spectrometry Detection (KSEC-MS): an Approach for Solution-Based Label-Free Kinetic Analysis of Protein-Small Molecule Interactions. Bao, J., Krylova, S.M., Cherney, L.T., Le Blanc, J.C.Y., Pribil, P., Johnson, P.E., Wilson, D.J., and Krylov, S.N. (2014) Analytical Chemistry, 86, 10016-10020 .
31. Quinine binding by the cocaine binding aptamer. Thermodynamic and hydrodynamic analysis of off-target binding. Reinstein, O., Yoo, M., Han C., Palmo, T., Beckham, S.A., Wilce, M.C.J., Johnson, P.E. (2013) Biochemistry, 52, 8652-8662.
30. Quantitative Affinity Electrophoresis of RNA-Small Molecule Interactions by Cross-Linking the Ligand to Acrylamide. Boodram, S.N., McCann, L.C., Organ, M.G., Johnson, P.E. (2013) Analytical Biochemistry, 442, 231-236.
29. Label-free solution-based kinetic study of aptamer-small-molecule interactions reveals how kinetics control equilibrium. Bao, J., Krylova, S.M., Reinstein, O., Johnson, P.E., Krylov, S.N. (2011) Analytical Chemistry, 83, 8387-8390.
28. Kinetic capillary electrophoresis with mass-spectrometry detection (KCE-MS) facilitates label-free solution-based kinetic analysis of protein-small molecule binding. Bao, J., Krylova, S.M., Wilson, D.J., Reinstein, O., Johnson, P.E., Krylov, S.N. (2011) ChemBioChem, 12, 2551-2554.
27. Engineering a Structure Switching Mechanism into a Steroid Binding Aptamer and Hydrodynamic Analysis of the Ligand Binding Mechanism. Reinstein, O., Neves, M.A.D., Saad, M., Boodram, S.N., Lombardo, S., Beckham, S.A., Brouwer, J., Audette, G.F., Groves, P., Wilce, M.C.J., Johnson, P.E. (2011) Biochemistry, 50, 9368-9376.
26. Identification of RNA-ligand interactions by affinity electrophoresis. Boodram, S.N., Cho, C.M., Tavares, T.J., Johnson, P.E. (2011) Analytical Biochemistry, 409, 54-58.
25. Finding the Path in an RNA Folding Landscape. Boodram, S.N., Johnson, P.E. (2010) Structure, 18, 1550-1551.
24. Defining the secondary structural requirements of a cocaine-binding aptamer by a thermodynamic and mutation study. Neves, M.A.D., Reinstein, O., Saad, M., Johnson, P.E. (2010) Biophysical Chemistry, 153, 9-16.
23. Thermodynamic and NMR Analysis of Inhibitor Binding to Dihydrofolate Reductase. Batruch, I., Javasky, E., Brown, E.D., Organ, M.G., Johnson, P.E. (2010) Bioorganic & Medicinal Chemistry, 18, 8485-8492.
22. Defining a stemlength-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR and calorimetry study. Neves, M.A.D., Reinstein, O., Johnson, P.E. (2010) Biochemistry, 49, 8478-8487.
21. Structure of the Cytosine-Cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin. Tavares, T.J., Beribisky, A.V., Johnson, P.E. (2009) RNA, 15, 911-922. full text
20. Enhanced NMR Signal Detection of Imino Protons in RNA Molecules Containing 3' Dangling Nucleotides. Amborski, A.N., Johnson, P.E. (2008) Journal of Biomolecular NMR, 40, 183-188.
20. Enhanced NMR Signal Detection of Imino Protons in RNA Molecules Containing 3' Dangling Nucleotides. Amborski, A.N., Johnson, P.E. (2008) Journal of Biomolecular NMR, 40, 183-188.
19. The Three-dimensional Structure of the Moorella thermoacetica Selenocysteine Insertion Sequence RNA Hairpin and its Interaction with the Elongation factor SelB. Beribisky, A.V., Tavares, T.J., Amborski, A.N., Motamed, M., Johnson, A.E., Mark, T.L., Johnson, P.E. (2007) RNA, 13, 1948-1956. full textÌý²¹²Ô»åÌýsupplemantary material
18. RNA Recognition by the Vts1 SAM Domain. Johnson, P.E., Donaldson, L.W. (2006) Nature Structural and Molecular Biology, 13, 177-178. full text
17. The NMR and X-ray Structures of the Saccharomyces cerevisiae Vts1 SAM Domain Define a Surface for the Recognition of RNA Hairpins. Aviv, A., Amborski, A.N., Zhao, X.S., Kwan, J.J. Johnson, P.E., Sicheri, F., Donaldson, L.W. (2006) Journal of Molecular Biology, 356, 274-279. full text
16. Assembly PCR Oligo Maker: A tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production.  Rydzanicz, R., Zhao, X. S., Johnson, P.E., (2005) Nucleic Acids Res., 33: W521-W525. full text
15. Identification of a novel non-carbohydrate molecule that binds to the ribosomal A-site RNA.  Maddaford, S.P., Motamed, M., Turner K., Choi, M.S.K., Ramnauth, J., Rakhit, S., Hudgins, R., Fabris, D., Johnson, P.E., (2004) Bioorganic and Medicinal Chemistry Letters, 14, 5987-5990. full text
Before York:
14. A Mechanism for Plus-Strand Transfer Enhancement by the HIV-1 Nucleocapsid Protein During Reverse Transcription. Johnson, P.E., Turner, R.B., Wu, Z.R., Hairston, L., Guo, J., Levin, J.G., Summers, M.F. (2000) Biochemistry, 39, 9084-9091 full text
13. The NMR structure of the MMTV nucleocapsid protein reveals unusual folding in the C-terminal zinc knuckle. Klein, D.J., Johnson, P.E., Zollars, E.S., De Guzman, R.N., Summers, M.F. (2000) Biochemistry, 39, 1604-1612. full text
12. Binding site analysis of cellulose-binding domain CBDN1 from endoglucanase C of Cellulomonas fimi by site-directed mutagenesis. Kormos, J., Johnson, P.E., Brun, E.,Tomme, P., McIntosh, L.P., Haynes, C.A., Kilburn, D.G., (2000) Biochemistry, 39, 8844-8852. full text
11. Structure and binding secificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi Endoglucanase C. Brun, E., Johnson, P.E., Creagh, A.L., Haynes, C.A., Tomme, P., Webster, P., Kilburn, D.G., McIntosh, L.P. (2000) Biochemistry, 39, 2445-2458. full text
10. The cellulose-binding domains from Cellulomonas fimi b-1,4-glucanase CenC bind nitroxide spin-labeled cellooligosaccharides in multiple orientations. Johnson, P.E., Brun, E., MacKenzie, L. Withers, S.G., McIntosh, L.P. (1999) Journal of Molecular Biology, 287, 609-625. full text
9. Calcium Binding By The N-Terminal Cellulose-Binding Domain From Cellulomonas fimi b-1,4-Glucanase CenC. Johnson, P.E., Creagh, A.L., Brun, E., Joe, K., Tomme, P., Haynes, C.A., McIntosh, L.P. (1998) Biochemistry, 37, 12772-12781. full text
8. Binding and stability of the N1 cellulose-binding domain of Cellulomonas fimi endoglucanase CenC. Creagh, A.L., Koska, J., Johnson, P.E., Joshi, M.D., Tomme, P., McIntosh, L.P., Kilburn, D.G., Haynes, C.A. (1998) Biochemistry, 37, 3529-3537. full text
7. Mechanisms of cellulases and xylanases Birsan C., Johnson P., Joshi M., MacLeod A., McIntosh L., Monem V., Nitz M., Rose D.R., Tull D., Wakarchuk W.W., Wang Q., Warren R.A., White A., Withers S.G. (1998) Biochem. Soc. Trans., 26 156-160.
6. Specific 15N, NH correlations for residues in 15±·,Ìý13C fractionally deuterated proteins that immediately follow methyl-containing amino acids. Muhandiram, D.R., Johnson, P.E., Yang, D., Zhang, O., McIntosh, L.P., Kay, L.E. (1997) Journal of Biomolecular NMR, 10, 283-288. full text
5. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by NMR spectroscopy. Johnson, P.E., Joshi, M.D., Tomme, P., Kilburn, D.G., McIntosh, L.P. (1996) Biochemistry, 35, 14381-14394. full text
4. Interaction of soluble cellooligosaccharides with the N-terminal cellulose-binding domain of Cellulomonas fimi CenC 2. NMR and ultraviolet absorption spectroscopy. Johnson, P.E., Tomme, P., Joshi, M.D., McIntosh, L.P. (1996) Biochemistry, 35, 13895-13906. full text
3. The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A 13C NMR study of Bacillus circulans xylanase. McIntosh, L.P., Hand, G., Johnson, P.E., Joshi, M., Kšrner, M., Plesniak, L.A., Zeiser, L.M., Wakarchuk, W., Withers, S. (1996) Biochemistry, 35, 9958-9966. full text
2. Cellulose-binding domains: versatile affinity tags for large scale purification, concentration and immobilization of fusion proteins. Tomme, P., Gilkes, N.R., Guarna, M.M., Haynes, C.A., Hasenwinkle, D., Jervis, E., Johnson, P., McIntosh, L., Miller Jr., R.C., Warren, R.A.J., Kilburn D.G. (1996) Annals of the New York Academy of Science, 799, 418-424.
1. Probing the role of the tryptophan residues in a cellulose-binding domain by chemical modification. Bray, M.R., Johnson P.E., Gilkes, N.R., McIntosh,. L.P. Kilburn, D.G., Warren, R.A.J. (1996) Protein Science, 5, 2311-2318.