How human serum albumin-selective DNA aptamer binds to bovine and canine serum albumins.
DNA aptamer
MD simulations
aptasensor
bovine serum albumin
canine serum albumin
human serum albumin
Journal
Biopolymers
ISSN: 1097-0282
Titre abrégé: Biopolymers
Pays: United States
ID NLM: 0372525
Informations de publication
Date de publication:
Mar 2021
Mar 2021
Historique:
revised:
12
01
2021
received:
15
09
2020
accepted:
14
01
2021
pubmed:
11
2
2021
medline:
26
10
2021
entrez:
10
2
2021
Statut:
ppublish
Résumé
Serum albumin (SA) is the most abundant carrier protein in blood. SA carries a diverse range of nutrients, drugs, and metal ions. It has wide clinical and biochemical applications. Human serum albumin (HSA) can be used as a biomarker for kidney and liver diseases. Aptasensor is one of potential HSA detection methods. HSA-specific aptamer was selected for HSA detection. In animals, bovine serum albumin (BSA) and canine serum albumins (CSA) share high sequence similarities to HSA. Thus, it is interesting to explore the possibility of using HSA-selective aptamer for BSA and CSA aptasensor. In this study, molecular dynamics (MD) simulations were initially employed to investigate the binding of aptamer to BSA and CSA in comparison to HSA. Like HSA, both BSA and CSA can bind aptamer, but different binding affinities are observed. BSA shows the tighter binding to aptamer than CSA. Domain III is found to be the aptamer-binding domain although no specific aptamer conformation is captured. However, in all cases, the aptamer utilizes the 3'-end to attach on an albumin surface. Both nucleobases and phosphate backbones on a DNA aptamer are important for albumin-aptamer complexation. Our results imply the possibility of using HSA-specific aptamer for BSA detection due to tighter binding observed, but may be less effective in CSA. However, the test in actual complicated condition must be further studied.
Substances chimiques
Aptamers, Nucleotide
0
Serum Albumin
0
Serum Albumin, Bovine
27432CM55Q
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e23421Subventions
Organisme : Development of Advance Researcher Competence System for Competitiveness in Agriculture and Food from Kasetsart University Research and Development Institute (KURDI)
ID : FF(KU)25.64
Organisme : National Nanotechnology Center
ID : P1751330
Organisme : National Science and Technology Development Agency (NSTDA)
ID : SCA-CO-2562-9727-TH
Organisme : Office of National Higher Education Science Research and Innovation policy council and PMUB
ID : B05F630035
Informations de copyright
© 2021 Wiley Periodicals LLC.
Références
T. Zhu, J. J. Du, W. B. Cao, J. L. Fan, X. J. Peng, Ind. Eng. Chem. Res. 2016, 55, 527.
T. A. Waldmann, W. D. Terry, J. Clin. Invest. 1990, 86, 2093.
G. A. Kaysen, N. W. Levin, Adv. Chronic Kidney Dis. 2004, 11, 241.
M. Cirillo, M. Laurenzi, P. Panarelli, M. Mancini, A. Zanchetti, N. G. De Santo, Kidney Int. 2004, 65, 2290.
M. Laurenzi, M. Cirillo, N. G. De Santo, Am. J. Kidney Dis. 2004, 43, A20.
Y. H. Chuang, Y. T. Chang, K. L. Liu, H. Y. Chang, T. R. Yew, Biosens. Bioelectron. 2011, 28, 368.
F. Eertmans, V. Bogaert, B. Puype, Anal. Methods-UK 2011, 3, 1296.
A. H. Liang, Z. J. Lu, Q. Y. Liu, X. H. Zhang, G. Q. Wen, Z. L. Jiang, RSC Adv. 2015, 5, 5711.
S. Choi, E. Y. Choi, H. S. Kim, S. W. Oh, Clin. Chem. 2004, 50, 1052.
S. Choi, E. Y. Choi, D. J. Kim, J. H. Kim, T. S. Kim, S. W. Oh, Clin. Chim. Acta 2004, 339, 147.
A. A. Pegoraro, W. Peracha, M. Hasnain, N. Ranginwala, M. Shaykh, A. K. Singh, J. A. Arruda, G. Dunea, Am. J. Kidney Dis. 2000, 35, 739.
S. Gao, G. Wei, S. Zhang, B. Zheng, J. Xu, G. Chen, M. Li, S. Song, W. Fu, Z. Xiao, W. Lu, Nat. Commun. 2019, 10, 2206.
A. D. Shao, Z. Q. Guo, W. H. Zhu, Nanomed.-Nanotechnol. 2016, 12, 516.
A. D. Shao, Z. Q. Guo, S. J. Zhu, S. Q. Zhu, P. Shi, H. Tian, W. H. Zhu, Chem. Sci. 2014, 5, 1383.
V. S. Jisha, K. T. Arun, M. Hariharan, D. Ramaiah, J. Am. Chem. Soc. 2006, 128, 6024.
J. C. Er, M. K. Tang, C. G. Chia, H. Liew, M. Vendrell, Y. T. Chang, Chem. Sci. 2013, 4, 2168.
A. Baldridge, S. H. Feng, Y. T. Chang, L. M. Tolbert, ACS Comb. Sci. 2011, 13, 214.
B. T. Doumas, W. A. Watson, H. G. Biggs, Clin. Chim. Acta 1971, 31, 87.
B. T. Doumas, T. Peters Jr.., Clin. Chim. Acta 1997, 258, 3.
V. Bush, R. G. Reed, Clin. Chem. 1987, 33, 821.
J. E. Gustafsson, Clin. Chem. 1976, 22, 616.
Y. J. Xu, M. M. Su, H. L. Li, Q. X. Liu, C. Xu, Y. S. Yang, H. L. Zhu, Anal. Chim. Acta 2018, 1043, 123.
S. Lee, D. B. Sung, S. Kang, S. Parameswaran, J. H. Choi, J. S. Lee, M. S. Han, Sensors (Basel) 2019, 19, 5298.
C. Tothova, O. Nagy, G. Kovac, Vet. Med.-Czech. 2016, 61, 475.
T. Stokol, J. M. Tarrant, J. M. Scarlett, Vet. Clin. Pathol. 2001, 30, 170.
P. A. Gentry, J. H. Lumsden, Vet. Clin. Pathol. 1978, 7, 12.
G. W. Osbaldiston, Br. Vet. J. 1972, 128, 386.
K. Muller, L. Brunnberg, Vet. Clin. Pathol. 2010, 39, 79.
W. Chawjiraphan, C. Apiwat, K. Segkhoonthod, K. Treerattrakoon, P. Pinpradup, N. Sathirapongsasuti, P. Pongprayoon, P. Luksirikul, P. Isarankura-Na-Ayudhya, D. Japrung, Spectrochim. Acta, Part A 2020, 231, 118128.
C. Apiwat, P. Luksirikul, P. Kankla, P. Pongprayoon, K. Treerattrakoon, K. Paiboonsukwong, S. Fucharoen, T. Dharakul, D. Japrung, Biosens. Bioelectron. 2016, 82, 140.
K. A. Majorek, P. J. Porebski, A. Dayal, M. D. Zimmerman, K. Jablonska, A. J. Stewart, M. Chruszcz, W. Minor, Mol. Immunol. 2012, 52, 174.
K. Yamada, K. Yokomaku, M. Kureishi, M. Akiyama, K. Kihira, T. Komatsu, Sci. Rep. 2016, 6, 36782.
S. Ketrat, D. Japrung, P. Pongprayoon, J. Mol. Graph. Model. 2020, 98, 107601.
W. Panman, D. Japrung, P. Pongprayoon, J. Biomol. Struct. Dyn. 2016, 35, 2328.
T. Awang, N. Wiriyatanakorn, P. Saparpakorn, D. Japrung, P. Pongprayoon, J. Biomol. Struct. Dyn. 2016, 35, 781.
P. Pongprayoon, M. P. Gleeson, J. Mol. Graph. Model. 2014, 54, 164.
P. Pongprayoon, T. Mori, Phys. Chem. Chem. Phys. 2018, 20, 3249.
T. E. Cheatham 3rd., P. Cieplak, P. A. Kollman, J. Biomol. Struct. Dyn. 1999, 16, 845.
E. Lindahl, B. Hess, D. van der Spoel, J. Mol. Model. 2001, 7, 306.
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins: Struct., Funct., Bioinf. 2006, 65, 712.
T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089.
G. Bussi, D. Donadio, M. Parrinello, J. Chem. Phys. 2007, 126, 14101.
W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 1996, 14, 33.
Z. Hazarika, A. N. Jha, ACS Omega 2020, 5, 170.
H. Malonga, J. F. Neault, H. Arakawa, H. A. Tajmir-Riahi, DNA Cell Biol. 2006, 25, 63.
H. Malonga, J. F. Neault, H. A. Tajmir-Riahi, DNA Cell Biol. 2006, 25, 393.
M. Lin, J. T. Guo, Nucleic Acids Res. 2019, 47, 11103.
Y. Mandel-Gutfreund, O. Schueler, H. Margalit, J. Mol. Biol. 1995, 253, 370.
N. M. Luscombe, S. E. Austin, H. M. Berman, J. M. Thornton, Genome Biol. 2000, 1, 1.
C. Rastogi, H. T. Rube, J. F. Kribelbauer, J. Crocker, R. E. Loker, G. D. Martini, O. Laptenko, W. A. Freed-Pastor, C. Prives, D. L. Stern, R. S. Mann, H. J. Bussemaker, Proc. Natl. Acad. Sci. U. S. A. 2018, 115, E3692.
W. Panman, D. Japrung, P. Pongprayoon, J. Biomol. Struct. Dyn. 2017, 35, 2328.
D. Lejeune, N. Delsaux, B. Charloteaux, A. Thomas, R. Brasseur, Proteins 2005, 61, 258.
A. N. Temiz, P. V. Benos, C. J. Camacho, Nucleic Acids Res. 2010, 38, 2134.
R. Rohs, X. Jin, S. M. West, R. Joshi, B. Honig, R. S. Mann, Annu. Rev. Biochem. 2010, 79, 233.
T. H. Dickey, S. E. Altschuler, D. S. Wuttke, Structure 2013, 21, 1074.
N. M. Luscombe, R. A. Laskowski, J. M. Thornton, Nucleic Acids Res. 2001, 29, 2860.
N. M. Luscombe, J. M. Thornton, J. Mol. Biol. 2002, 320, 991.
L. I. Alinovskaya, S. E. Sedykh, N. V. Ivanisenko, S. E. Soboleva, G. A. Nevinsky, Biol. Chem. 2018, 399, 347.