Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations
Autoři:
Nathalie Casanova-Morales aff001; Nataniel L. Figueroa aff001; Karol Alfaro aff002; Felipe Montenegro aff003; Nelson P. Barrera aff003; J. R. Maze aff001; Christian A. M. Wilson aff004; Pablo Conejeros aff002
Působiště autorů:
Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
aff001; CIGREN. Instituto de Biología. Facultad de Ciencias. Universidad de Valparaíso, Valparaíso, Chile
aff002; Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
aff003; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
aff004; Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
aff005
Vyšlo v časopise:
PLoS ONE 14(11)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0222468
Souhrn
Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single–molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1–aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer–Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.
Klíčová slova:
Simulation and modeling – Toxins – Lasers – Biochemical simulations – Molecular dynamics – Microfluidics – Magnesium – Microspheres
Zdroje
1. Mons MN, van Egmond HP, Speijers GJa. Paralytic shellfish poisoning: A review; 1998.
2. Wang DZ. Neurotoxins from Marine Dinoflagellates: A Brief Review. Mar Drugs. 2008;6(2):349–371. doi: 10.3390/md20080016 18728731
3. Alexander J, Auðunsson GA, Benford D, Cockburn A, Dogliotti E, Domenico AD, et al. Perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA) and their salts—Scientific opinion of the Panel on Contaminants in the Food chain. EFSA J. 2008;653:1–131.
4. Avaria S, Cáceres M, Muñoz P, Palma S, Vera P. Plan nacional sobre floraciones de algas nocivas en Chile. Comité Oceanográfico Nacional; 1999.
5. Levin RE. Paralytic shellfish toxins: their origin, characteristics and methods of detection: a review. J Food Biochem. 1991;15(6):405–417. doi: 10.1111/j.1745-4514.1991.tb00425.x
6. Sellner KG, Doucette GJ, Kirkpatrick GJ. Harmful algal blooms: causes, impacts and detection. J Ind Microbiol Biotechnol. 2003;30(7):383–406. doi: 10.1007/s10295-003-0074-9 12898390
7. Usleber E, Dietrich R, Bürk C, Schneider E, Märtlbauer E. Immunoassay methods for paralytic shellfish poisoning toxins. J AOAC Int. 2001;84(5):1649–56. 11601488
8. Handy SM, Yakes BJ, DeGrasse Ja, Campbell K, Elliott CT, Kanyuck KM, et al. First report of the use of a saxitoxin–protein conjugate to develop a DNA aptamer to a small molecule toxin. Toxicon. 2013;61:30–37. doi: 10.1016/j.toxicon.2012.10.015 23142073
9. Zheng X, Hu B, Gao SX, Liu DJ, Sun MJ, Jiao BH, et al. A saxitoxin-binding aptamer with higher affinity and inhibitory activity optimized by rational site-directed mutagenesis and truncation. Toxicon. 2015;101:41–47. doi: 10.1016/j.toxicon.2015.04.017 25937337
10. Alfaro K, Bustos P, O’Sullivan C, Conejeros P. Facile and cost-effective detection of saxitoxin exploiting aptamer structural switching. Food Technol Biotechnol. 2015;53(3):337–341. doi: 10.17113/ftb.53.03.15.3911 27904366
11. Tombelli S, Mascini M. Aptamers Biosensors for Pharmaceutical Compounds. Comb Chem High Throughput Screen. 2010;13(7):641–649. doi: 10.2174/1386207311004070641 20426747
12. Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (80-). 1990;249(4968):505–510. doi: 10.1126/science.2200121
13. Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990;346(6287):818–22. doi: 10.1038/346818a0 1697402
14. Schochetman G, Ou CY, Jones WK. Polymerase chain reaction. J Infect Dis. 1988;158(6):1154–7. doi: 10.1093/infdis/158.6.1154 2461996
15. Fahrner RL, Knudsen HL, Basey CD, Galan W, Feuerhelm D, Vanderlaan M, et al. Industrial Purification of Pharmaceutical Antibodies: Development, Operation, and Validation of Chromatography Processes. Biotechnol Genet Eng Rev. 2001;18(1):301–327. doi: 10.1080/02648725.2001.10648017 11530694
16. Tombelli S, Minunni M, Mascini M. Aptamers-based assays for diagnostics, environmental and food analysis. Biomol Eng. 2007;24(2):191–200. doi: 10.1016/j.bioeng.2007.03.003 17434340
17. Stojanovic MN, de Prada P, Landry DW. Aptamer-Based Folding Fluorescent Sensor for Cocaine. J Am Chem Soc. 2001;123(21):4928–4931. doi: 10.1021/ja0038171 11457319
18. Song KM, Lee S, Ban C. Aptamers and Their Biological Applications. Sensors. 2012;12(12):612–631. doi: 10.3390/s120100612 22368488
19. Han K, Liang Z, Zhou N. Design Strategies for Aptamer-Based Biosensors. Sensors. 2010;10(5):4541–4557. doi: 10.3390/s100504541 22399891
20. Chen H, Meisburger SP, Pabit SA, Sutton JL, Webb WW, Pollack L. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA. Proc Natl Acad Sci U S A. 2012;109(3):799–804. doi: 10.1073/pnas.1119057109 22203973
21. Ashkin A. Acceleration and Trapping of Particles by Radiation Pressure. Phys Rev Lett. 1970; 24(4):156–159. doi: 10.1103/PhysRevLett.24.156
22. Bustamante C, Smith SB. Light-force sensor and method for measuring axial optical-trap forces from changes in light momentum along an optic axis. US 7,133,132 B2; 2006.
23. Smith SB, Cui Y, Bustamante C. Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules. Science (80-). 1996;271(5250):795–799. doi: 10.1126/science.271.5250.795
24. Bustamante C, Smith SB, Liphardt J, Smith D. Single-molecule studies of DNA mechanics. Curr Opin Struct Biol. 2000;10(3):279–85. doi: 10.1016/S0959-440X(00)00085-3 10851197
25. Chi Q, Wang G, Jiang J. The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory. Phys A Stat Mech its Appl. 2013;392(5):1072–1079. doi: 10.1016/j.physa.2012.09.022
26. Alemany A, Ritort F. Determination of the elastic properties of short ssDNA molecules by mechanically folding and unfolding DNA hairpins. Biopolymers. 2014;101(12):1193–1199. doi: 10.1002/bip.22533 25091120
27. Brandao MM, Fontes A, Barjas-Castro ML, Barbosa LC, Costa FF, Cesar CL, et al. Optical tweezers for measuring red blood cell elasticity: application to the study of drug response in sickle cell disease. Eur J Haematol. 2003;70(4):207–211. doi: 10.1034/j.1600-0609.2003.00027.x 12656742
28. Westfall PH. Resampling-based multiple testing:. North. 1989; p. 1359–1364.
29. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–802. doi: 10.1002/jcc.20289 16222654
30. Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, Mackerell AD. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput. 2012;8(1):348–362. doi: 10.1021/ct200723y 22368531
31. Zheng G, Lu XJ, Olson WK. Web 3DNA–a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res. 2009;37(Web Server):W240–W246. doi: 10.1093/nar/gkp358 19474339
32. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–3415. doi: 10.1093/nar/gkg595 12824337
33. Darden T, York D, Pedersen L. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98(12):10089. doi: 10.1063/1.464397
34. Ryckaert JP, Ciccotti G, Berendsen HJ. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977; 23: 327–341. doi: 10.1016/0021-9991(77)90098-5
35. Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: The Langevin piston method. J Chem Phys. 1995;103(11):4613. doi: 10.1063/1.470648
36. Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14(1):33–38. doi: 10.1016/0263-7855(96)00018-5 8744570
37. Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K. Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J Chem Phys. 2003;119(6):3559–3566. doi: 10.1063/1.1590311
38. McFail-Isom L, Shui X, Williams LD. Divalent Cations Stabilize Unstacked Conformations of DNA and RNA by Interacting with Base Π Systems. Biochemistry. 1998;37(49):17105–17111. doi: 10.1021/bi982201+ 9860822
39. Frauendorf C, Jäschke A. Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem. 2001;9(10):2521–2524. doi: 10.1016/s0968-0896(01)00027-x 11557338
40. Stojanovic MN, de Prada P, Landry DW. Fluorescent Sensors Based on Aptamer Self-Assembly. J Am Chem Soc. 2000;122(46):11547–11548. doi: 10.1021/ja0022223 29048887
41. Gopinath SCB. Methods developed for SELEX. Anal Bioanal Chem. 2006;387(1):171–182. doi: 10.1007/s00216-006-0826-2 17072603
42. Wang DY, Sen D. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. J Mol Biol. 2001;310(4):723–734. doi: 10.1006/jmbi.2001.4811 11453683
43. Baldrich E, Restrepo A, O’Sullivan CK. Aptasensor Development: Elucidation of Critical Parameters for Optimal Aptamer Performance. Anal Chem. 2004;76(23):7053–7063. doi: 10.1021/ac049258o 15571359
44. Mir M, Katakis I. Aptamers as elements of bioelectronic devices. Mol Biosyst. 2007;3(9):620. doi: 10.1039/b708858b 17700862
45. Navani N, Li Y. Nucleic acid aptamers and enzymes as sensors. Curr Opin Chem Biol. 2006;10(3):272–281. doi: 10.1016/j.cbpa.2006.04.003 16678470
46. Le Floch F, Ho HA, Leclerc M. Label-Free Electrochemical Detection of Protein Based on a Ferrocene-Bearing Cationic Polythiophene and Aptamer. Anal Chem. 2006;78(13):4727–4731. doi: 10.1021/ac0521955 16808489
47. Cheng AKH, Ge B, Yu HZ. Aptamer-Based Biosensors for Label-Free Voltammetric Detection of Lysozyme. Anal Chem. 2007;79(14):5158–5164. doi: 10.1021/ac062214q 17566977
48. Yang CJ, Jockusch S, Vicens M, Turro NJ, Tan W. Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc Natl Acad Sci. 2005;102(48):17278–17283. doi: 10.1073/pnas.0508821102 16301535
49. Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H. Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett. 2006;16(16):4381–4384. doi: 10.1016/j.bmcl.2006.05.054 16757168
50. Hong KL, Sooter LJ. Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BioMed Research International 2015; Article ID 419318 doi: 10.1155/2015/419318
51. Kerrin ES, White RL, Quilliam MA. Quantitative determination of the neurotoxin β-N-methylamino-L-alanine (BMAA) by capillary electrophoresis–tandem mass spectrometry. Anal Bioanal Chem 2017, 409(6): 1481–1491 doi: 10.1007/s00216-016-0091-y 27909777
Článok vyšiel v časopise
PLOS One
2019 Číslo 11
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Nejasný stín na plicích – kazuistika
- Masturbační chování žen v ČR − dotazníková studie
- Je Fuchsova endotelová dystrofie rohovky neurodegenerativní onemocnění?
- Fixní kombinace paracetamol/kodein nabízí synergické analgetické účinky
Najčítanejšie v tomto čísle
- A daily diary study on maladaptive daydreaming, mind wandering, and sleep disturbances: Examining within-person and between-persons relations
- A 3’ UTR SNP rs885863, a cis-eQTL for the circadian gene VIPR2 and lincRNA 689, is associated with opioid addiction
- A substitution mutation in a conserved domain of mammalian acetate-dependent acetyl CoA synthetase 2 results in destabilized protein and impaired HIF-2 signaling
- Molecular validation of clinical Pantoea isolates identified by MALDI-TOF