Label-free amino acid identification based on tRNA charging in a cavity and AMP blockade in a nanopore
作者： G. Sampath
DOI: 10.1101/2020.06.25.170803
关键词:
摘要: Label-free identification of amino acids (AAs) based on superspecific transfer RNAs (tRNAs) and amino-acyl tRNA synthetase (AARS) is explored. Molecules a specific AA, its cognate AARS, adenosine triphosphate (ATP) from reservoir are confined to micro-sized cavity by hydraulic pressure counter the effects diffusion. In this space in gets charged with AA monophosphate (AMP) released. The products transferred an electrolytic cell nanopore where AMP, ATP cause current blockades different sizes. If AMP-sized blockade occurs it means that molecule has been identifies AA; otherwise procedure repeated AARS until identified. Unlike most other nanopore-based methods, there no need for precise measurement levels. efficacy assessed simulating movement particles reservoir-cavity structure analyzing occur nanopore. former probability reactants escaping found be near 0. latter error identifying AMP less than 10% worst case (which largest volume namely Tryptophan). Detailed information data provided Supplementary File.
sci-hub.st 参考文章(52)
Richard J Simpson, Richard J Simpson, Proteins and proteomics : a laboratory manual Cold Spring Harbor Laboratory Press. ,(2003)
Stephen J. PERKINS, Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences. FEBS Journal. ,vol. 157, pp. 169- 180 ,(1986) , 10.1111/J.1432-1033.1986.TB09653.X
Vincent Stroobant, Edmond de Hoffmann, Julie Trottier, Jean Joseph Charette, Mass Spectrometry: Principles and Applications ,(2002)
Michael Zwolak, Massimiliano Di Ventra, Colloquium: Physical approaches to DNA sequencing and detection Reviews of Modern Physics. ,vol. 80, pp. 141- 165 ,(2008) , 10.1103/REVMODPHYS.80.141
Kyle T. Brady, Joseph E. Reiner, Improving the prospects of cleavage-based nanopore sequencing engines Journal of Chemical Physics. ,vol. 143, pp. 074904- 074904 ,(2015) , 10.1063/1.4928647
Jiandong Feng, Ke Liu, Roman D. Bulushev, Sergey Khlybov, Dumitru Dumcenco, Andras Kis, Aleksandra Radenovic, Identification of single nucleotides in MoS2 nanopores Nature Nanotechnology. ,vol. 10, pp. 1070- 1076 ,(2015) , 10.1038/NNANO.2015.219
Michael Ibba, Dieter Söll, The renaissance of aminoacyl‐tRNA synthesis EMBO reports. ,vol. 2, pp. 382- 387 ,(2001) , 10.1093/EMBO-REPORTS/KVE095
Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, Cees Dekker, Slowing down DNA translocation through a nanopore in lithium chloride. Nano Letters. ,vol. 12, pp. 1038- 1044 ,(2012) , 10.1021/NL204273H
Aleksandar P. Ivanov, Paolo Actis, Peter Jönsson, David Klenerman, Yuri Korchev, Joshua B. Edel, On-demand delivery of single DNA molecules using nanopipets. ACS Nano. ,vol. 9, pp. 3587- 3595 ,(2015) , 10.1021/ACSNANO.5B00911
Ranulu Samanthi S. de Zoysa, Dilani A. Jayawardhana, Qitao Zhao, Deqiang Wang, Daniel W. Armstrong, Xiyun Guan, Slowing DNA translocation through nanopores using a solution containing organic salts. Journal of Physical Chemistry B. ,vol. 113, pp. 13332- 13336 ,(2009) , 10.1021/JP9040293