A computationally designed DNA aptamer template with specific binding to phosphatidylserine

Nucleic Acid Therapeutics

Volumn 23, Issue 6, 2013, Pages 418-426

  Ashrafuzzaman, Md ^a,b   Tseng, Chih Yuan ^a   Kapty, Janice ^a   Mercer, John R ^a   Tuszynski, Jack A ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b KING SAUD UNIVERSITY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DNA; PHOSPHATIDYLSERINE;

ARTICLE; BINDING AFFINITY; COMPUTER MODEL; CONTROLLED STUDY; DNA BINDING; DNA TEMPLATE; ENTROPY; IN VITRO STUDY; PRIORITY JOURNAL; SEED AND GROW STRATEGY;

APOPTOSIS; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; ENTROPY; LIPOSOMES; MOLECULAR DOCKING SIMULATION; NUCLEIC ACID CONFORMATION; PHOSPHATIDYLSERINES; SPECTROMETRY, FLUORESCENCE;

EID: 84890371407     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2013.0415     Document Type: Article

References (44)

1. ASHRAFUZZAMAN, M., TSENG, C-Y., DUSZYK, M., and TUSZYNSKI, J. (2012). Chemotherapy drugs form ion pores in membranes due to physical interactions with lipids. Chem. Biol. Drug. Des. 80, 992-1002
2. ASHRAFUZZAMAN, M., and TUSZYNSKI, J. (2012). Regulation of channel function due to coupling with a lipid bilayer. J. Comput. Theor. Nanosci. 9, 564-570
3. BLANKENBERG, F.G. (2009). Imaging the molecular signatures of apoptosis and injury with radiolabeled annexin V. Proc. Am.Thorac. Soc. 6, 469-476
4. BOERSMA, H.H., KIETSELAER, B.L., STOLK, L.M., BENNAGHMOUCH, A., HOFSTRA, L., NARULA, J., HEIDENDAL, G.A., and REUTELINGSPERGER, C.P. (2005). Past, present, and future of annexin A5: From protein discovery to clinical applications. J. Nucl. Med. 46, 2035-2050
5. CAMPANA, V., ZENTILIN, L., MIRABILE, I., KRANJC, A., CASANOVA, P., GIACCA, M., PRUSINER, S.B., LEGNAME, G., and ZURZOLO, C. (2009). Development of antibody fragments for immunotherapy of prion diseases. Biochem. J. 418, 507-515
6. CASE, D.A., DARDEN, T.A., CHEATHAM, T.E. III, SIMMERLING, C.L., WANG, J., DUKE, R.E., LUO, R., CROWLEY, M., WALKER, R.C., ZHANG, W., et al. (2008). AMBER 10. (University of California, San Francisco
7. CASE, D.A., DARDEN, T.A., CHEATHAM, T.E III, SIMMERLING, C.L., WANG, J., DUKE, R.E., LUO, R., CROWLEY, M., WALKER, R.C., ZHANG, W., et al. (2010). AMBER 11. (University of California, San Francisco
8. CATICHA, A. (2004). Relative entropy and inductive inference. In: Bayesian Inference and Maximum Entropy Methods in Science and Engineering. G. Erickson, Y. Zhai, ed. AIP Conf. Proc. 707 (American Institute of Physics, Melville, New York), pp. 75-96
9. CATICHA, A., and GIFFIN, A. (2007). Updating probabilities. In: Bayesian Inference and Maximum Entropy Methods in Science and Engineering. K. H. Knuth, A. Caticha, J. L. Center, A. Giffin, C. C. Rodriguez, ed. AIP Conf. Proc. 954 (American Institute of Physics, Melville, New York), pp. 74-84
10. CHEN, C-C., TSENG, C-Y., and DONG, J-J. (2007). New entropy-based method for variables selection and its application to the debris flow hazard assessment. Eng. Geol. 94, 19-24
11. CHIESA, R., DRISALDI, B., QUAGLIO, E., MIGHELI, A., PICCARDO, P., GHETTI, B., and HARRIS, D.A. (2000). Accumulation of protease-resistant prion protein (PrP) and apoptosis of cerebellar granule cells in transgenic mice expressing a PrP insertional mutation. Proc. Natl. Acad. Sci. 97, 5574-5579
12. ELMORE, S. (2007). Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495-516
13. GOUTELLE, S., MAURIN, M., ROUGIER, F., BARBAUT, X., BOURGUIGNON, L., DUCHER, M., and MAIRE, P. (2008). The Hill equation: A review of its capabilities in pharmacological modeling. Fundam. Clin. Pharmacol. 22, 633-648
14. HAMULA, C.L.A., GUTHRIE, J.W., ZHANG, H., LI, X.F., and CHRIS LE, X. (2006). Selection and analytical applications of aptamers. Trends Anal. Chem. 25, 681-691
15. HEPPNER, F.L., and AGUZZI, A. (2004). Recent developments in prion immunotherapy. Curr. Opin. Immunol. 16, 594-598
16. HOPE, M.J., BALLY, M.B., MAYER, L.D., JANOFF, A.S., and CULLIS, P.R. (1986). Generation of multilamellar and unilamellar phospholipid vesicles. Chem. Phys. Lipids 40, 89-107
17. HUMPHREY, W., DALKE, A., and SCHULTEN, K. (1996). VMD: Visual molecular dynamics. J. Mol. Graph 14, 33-38
18. JAMES, W. (2000). Aptamers. In: Encyclopedia of Analytical Chemistry. R. A. Meyers, ed. (John Wiley & Sons, Ltd., Chichester), pp. 4878-4871
19. JAMES, W. (2007). Aptamers in the virologists' toolkit. J. Gen.Virol. 88, 351-364
20. JAYNES, E.T. (1957a) Information theory and statistical mechanics. Phys. Rev. 106, 620-630
21. JAYNES, E.T. (1957b) Information theory and statistical mechanics II. Phys. Rev. 108, 171-190
22. KAPTY, J., BANMAN, S., GOPING, I.S., and MERCER, J.R. (2012). Evaluation of Phosphatidylserine-Binding Peptides Targeting Apoptotic Cells. J. Biomol. Screen. 17, 1293-1301
23. KEEFE, A.D., PAI, S., and ELINGTON, A. (2010). Aptamers as therapeutics. Nature Rev. Drug Discov. 9, 537-550
24. KERR, J.F., WYLLIE, A.H., and CURRIE, A.R. (1972). Apoptosis: A basic biological phenomenon with wide-ranging implications in tissue kinetics. Br. J. Cancer 4, 239-257
25. LAO, Y.H., PECK, K., and CHEN, L.C. (2009). Enhancement of aptamer microarray sensitivity through spacer optimization and avidity effect. Anal. Chem. 81, 1747-1754
26. MARTIN, S.J.,; REUTELINGSPERGER, C.P., MCGAHON, A.J., RADER, J.A., VAN SCHIE, R.C., LAFACE, D.M., and GREEN, D.R. (1995). Early redistribution of plasma membrane phosphatidylserine is a general feature of apoptosis regardless of the initiating stimulus: Inhibition by overexpression of Bcl-2 and Abl. J. Exp. Med. 182, 1545-1556
27. NIMJEE, S.M., RUSCONI, C.P., and SULLENGER, B.A. (2005). Aptamers: An emerging class of therapeutics. Annu. Rev. Med. 56, 555-583
28. PROSKE, D., GILCH, S., WOPFNER, F., SCHÄTZL, H.M., WINNACKER, E.L., and FAMULOK, M. (2002). Prion-proteinspecific aptamer reduces PrPSc formation. ChemBioChem 3, 717-725
29. QUADRIO, I., PERRET-LIAUDET, A., and KOVACS, G.G. (2011). Molecular diagnosis of human prion disease. Expert. Opin. Med. Diag. 5, 291-230
30. RASTOGI, R.P., RICHA, and SINHA, R.P. (2009). Apoptosis: Molecular mechanisms and pathogenicity EXCLI. J. 8, 155-181
31. RHIE, A., KIRBY, L., SAYER, N., WELLESLEY, R., DISTERER, P., SYLVESTER, I., GILL, A., HOPE, J., JAMES, W., and TAHIRI-ALAOUI, A. (2003). Characterization of 2-fluoro-RNA aptamers that bind preferentially to disease-Associated conformations of prion protein and inhibit conversion. J. Bio. Chem. 278, 39697-39705
32. ROBINSON, P.J., and PINHEIRO, T.J. (2010). Phospholipid composition of membranes directs prions down alternative aggregation pathways. Biophys. J. 98, 1520-1528
33. SHORE, J.E., and JOHNSON, R.W. (1980). Axiomatic derivation of the principle of maximum entropy and the principle of minimum cross entropy. IEEE Trans. Inf. Theory 26, 26-37
34. SHORE, J.E., and JOHNSON R.W. (1981). Properties of crossentropy minimization. IEEE Trans. Inf. Theory 27, 472-482
35. SMRZ, D., LEBDUSKA, P., DRÁ BEROVÁ, L., KORB, J., and DRÁ BER, P. (2008). Engagement of phospholipid scramblase 1 in activated cells: Implication for phosphatidylserine externalization and exocytosis. J. Biol. Chem. 283, 10904-10918
36. THELLUNG, S., CORSARO, A., VILLA, V., SIMI, A., VELLA, S., PAGANO, A., and FLORIO, T. (2011). Human PrP90-231-induced cell death is associated with intracellular accumulation of insoluble and protease-resistant macroaggregates and lysosomal dysfunction. Cell Death Dis. 2, e138
37. TSENG, C-Y. (2006). Entropic criterion for model selection. Physica A 370, 530-538
38. TSENG, C-Y., and Caticha, A. (2008). Using relative entropy to find optimal approximations: An application to simple fluids. Physica A 387, 6759-6770
39. TSENG, C-Y., ASHRAFUZZAMAN, MD, MANE, J., KAPTY, J., MERCER, J., and TUSZYNSKI, J. (2011). Entropic fragment based approach to aptamer design. Chem. Biol. Drug Design 78, 1-13
40. TUERK, C., and GOLD, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510
41. VAN MEER, G., VOELKER, D.R., and FEIGENSON, G.W. (2008). Membrane lipids: Where they are and how they behave. Nature Rev. Mol. Cell Biol. 9, 112-124
42. WANG, J., WOLF, R.M., CALDWELL, J.W., KOLLMAN, P.A., and CASE, D.A. (2004). Development and testing of a general AMBER force field. J. of Comp. Chem. 25, 1157-1174
43. WANG, J., WANG, W., KOLLMAN, P.A., and CASE, D.A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph Model 25, 247-260
44. WEINBERG, R.A. (2007). The biology of cancer. (Garlan Science, New York