scholarly journals Coarse-grained model of nucleic acid bases

2009 ◽  
pp. n/a-n/a ◽  
Author(s):  
Maciej Maciejczyk ◽  
Aleksandar Spasic ◽  
Adam Liwo ◽  
Harold A. Scheraga
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Nucleic Acid Bases ◽  
Coarse Grained Model

scholarly journals Understanding DNA interactions in crowded environments with a coarse-grained model

2020 ◽  
Vol 48 (19) ◽  
pp. 10726-10738
Author(s):  
Fan Hong ◽  
John S Schreck ◽  
Petr Šulc
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Strand Displacement ◽  
Dna Duplex ◽  
Kinetics And Thermodynamics ◽  
Coarse Grained Model ◽  
Dna Strand Displacement ◽  
Nucleic Acid Interactions ◽  
Crowded Environments ◽  
Crowded Environment

Abstract Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.

scholarly journals Understanding DNA interactions in crowded environments with a coarse-grained model

2020 ◽  
Author(s):  
Fan Hong ◽  
John S. Schreck ◽  
Petr Šulc
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Strand Displacement ◽  
Dna Duplex ◽  
Kinetics And Thermodynamics ◽  
Coarse Grained Model ◽  
Dna Strand Displacement ◽  
Nucleic Acid Interactions ◽  
Crowded Environments ◽  
Crowded Environment

Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.

scholarly journals Coarse-grained nucleic acid–protein model for hybrid nanotechnology

Soft Matter ◽  
2021 ◽  
Author(s):  
Jonah Procyk ◽  
Erik Poppleton ◽  
Petr Šulc
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Nanoscale Structures ◽  
Analysis And Design ◽  
Coarse Grained Model ◽  
Protein Model ◽  
Acid Protein ◽  
Hybrid Nanotechnology ◽  
Hybrid Dna

A coarse-grained model for analysis and design of hybrid DNA-protein nanoscale structures.

scholarly journals Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

2021 ◽  
Author(s):  
Yingnan Deng ◽  
Yuanhang Tan ◽  
Linghao Zhang ◽  
Chunyi Zhang ◽  
Xin Su
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Tumor Biomarker ◽  
Dna Nanostructures ◽  
Stimuli Responsive ◽  
Reaction Products ◽  
Coarse Grained Model ◽  
Sensitivity And Selectivity ◽  
Dna Nanotubes ◽  
Enzyme Recognition

Abstract The reactivity of DNA modifying enzymes on their natural nucleic acid substrates has been fully understood. However, their reactivity on self-assembled nanostructures of nucleic acid is complicated and unpredictable. Here, we employed the molecular dynamic simulation to forecast the reactivity of tumor biomarker enzymes on DNA nanotubes by coarse grained model. It is found that the enzyme accessibility and the potential energy of the reaction products co-determine the structural change of DNA nanotubes. The reactivity can be regulated by the position of enzyme recognition site. According to the simulation results, stimuli-responsive drug nanocarrier with superior sensitivity and selectivity was developed. Drug payloads released in cancer cells is 3.7~5.5-fold higher than that in normal cells. The DNA nanocarrier equipped with cancer-specific aptamer AS1411 is used to deliver doxorubicin (DOX) to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. This work provides new insights into the enzymatic reactivity of DNA nanostructures enriching the library of DNA-based reactions and heralding broad applications in nanomedicine.

Sign in / Sign up

Export Citation Format

Share Document