scholarly journals DNA barcode by flossing through a cylindrical nanopore

RSC Advances ◽  
2021 ◽  
Vol 11 (34) ◽  
pp. 20781-20787
Author(s):  
Swarnadeep Seth ◽  
Aniket Bhattacharya
Keyword(s):  
Dna Barcoding ◽  
Brownian Dynamics ◽  
Dwell Time ◽  
Dna Barcode ◽  
Time Measurement ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation ◽  
Recursive Scheme ◽  
Dna Backbone ◽  
Protein Tags

We report a method for DNA barcoding from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive scheme to improve the measurements to almost 100% accuracy.

scholarly journals DNA barcodes using a double nanopore system

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Swarnadeep Seth ◽  
Aniket Bhattacharya
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dna Barcodes ◽  
Brownian Dynamics Simulation ◽  
Simulation Data ◽  
Broad Distribution ◽  
Coarse Grained Model ◽  
Protein Tag ◽  
Protein Tags

AbstractThe potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain’s backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.

Brownian dynamics simulation of diffusion‐influenced bimolecular reactions

1984 ◽  
Vol 80 (4) ◽  
pp. 1517-1524 ◽  
Author(s):  
Scott H. Northrup ◽  
Stuart A. Allison ◽  
J. Andrew McCammon
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation ◽  
Bimolecular Reactions
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