Publications - The Johnson Lab

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. doi

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. doi

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 doi

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. doi

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. link

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. link

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. doi

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. link

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. doi

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. doi

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. doi

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. doi

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. doi

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. doi

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. doi

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. doi

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. doi

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. link

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. doi

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. doi

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. link

45. Isothermal titration calorimetry studies of aptamer-small molecule interactions: practicalities and pitfalls. Slavkovic, S. and Johnson, P.E. (2018) Aptamers, 2, 45-51. link

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. link

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. doi

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. doi

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 doi

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. doi

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 link

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. abstract or link

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 abstract

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 abstract

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 abstract

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 abstract

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. abstract

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 . abstract

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. abstract

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. abstract

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. abstract

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. abstract

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. abstract

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. abstract

25. Finding the Path in an RNA Folding Landscape. Boodram, S.N., Johnson, P.E. (2010) Structure, 18, 1550-1551. abstract

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. abstract

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. abstract

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. abstract

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. abstract

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 text and supplemantary 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 CBD_N1 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 ¹⁵N, ¹³C 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 pK_a 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. abstract

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. abstract