Coarse-grained modeling of DNA-RNA hybrids

被引：0

作者：

Ratajczyk, Eryk J. ^{[1
,2
]}

Sulc, Petr ^{[3
,4
,5
]}

Turberfield, Andrew J. ^{[1
,2
]}

Doye, Jonathan P. K. ^{[6
]}

Louis, Ard A. ^{[7
]}

机构：

[1] Univ Oxford, Dept Phys, Clarendon Lab, Parks Rd, Oxford OX1 3PU, England

[2] Univ Oxford, Kavli Inst Nanosci Discovery, Dorothy Crowfoot Hodgkin Bldg, South Parks Rd, Oxford OX1 3QU, England

[3] Arizona State Univ, Sch Mol Sci, 1001 South McAllister Ave, Tempe, AZ 85281 USA

[4] Arizona State Univ, Biodesign Inst, Ctr Mol Design & Biomimet, 1001 South McAllister Ave, Tempe, AZ 85281 USA

[5] Tech Univ Munich, Sch Nat Sci, Dept Biosci, D-85748 Garching, Germany

[6] Univ Oxford, Dept Chem, Phys & Theoret Chem Lab, South Parks Rd, Oxford OX1 3QZ, England

[7] Univ Oxford, Rudolf Peierls Ctr Theoret Phys, 1 Keble Rd, Oxford OX1 3NP, England

来源：

JOURNAL OF CHEMICAL PHYSICS | 2024年 / 160卷 / 11期

基金：

美国国家科学基金会; 英国工程与自然科学研究理事会;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; THERMODYNAMIC PARAMETERS; CRYSTAL-STRUCTURE; STRANDED-DNA; STABILITY; NANOSTRUCTURES; DISPLACEMENT; RECOGNITION; NANOROBOT; DUPLEXES;

D O I：

10.1063/5.0199558

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.

引用

页数：14

共 50 条

[21] Coarse-Grained Modeling for Macromolecular Chemistry
Karimi-Varzaneh, Hossein Ali
Mueller-Plathe, Florian
MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY, 2012, 307 : 295 - +
[22] Coarse-Grained Prediction of RNA Loop Structures
Liu, Liang
Chen, Shi-Jie
PLOS ONE, 2012, 7 (11):
[23] Fast coarse-grained model for RNA titration
Barroso da Silva, Fernando Luis
Derreumaux, Philippe
Pasquali, Samuela
JOURNAL OF CHEMICAL PHYSICS, 2017, 146 (03):
[24] Development and Applications of Coarse-Grained Models for RNA
Hyeon, Changbong
Denesyuk, Natalia A.
Thirumalai, D.
ISRAEL JOURNAL OF CHEMISTRY, 2014, 54 (8-9) : 1358 - 1373
[25] Coarse-grained dynamic RNA titration simulations
Pasquali, S.
Frezza, E.
Barroso da Silva, F. L.
INTERFACE FOCUS, 2019, 9 (03)
[26] Martini Coarse-Grained Force Field for RNA
Uusitalo, Jaakko J.
Ingolfsson, Helgi I.
Marrink, Siewert J.
Faustino, Ignacio
BIOPHYSICAL JOURNAL, 2018, 114 (03) : 437A - 437A
[27] Coarse-grained modeling of DNA-protein interactions helps elucidate DNA compaction
Sulc, Petr
BIOPHYSICAL JOURNAL, 2024, 123 (18) : 2961 - 2963
[28] Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Wei, Zonghui
Luijten, Erik
JOURNAL OF CHEMICAL PHYSICS, 2015, 143 (24):
[29] DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
Ouldridge, Thomas E.
Louis, Ard A.
Doye, Jonathan P. K.
PHYSICAL REVIEW LETTERS, 2010, 104 (17)
[30] Modeling long RNA structure and dynamics with the generalized SIS-RNA coarse-grained model
Hori, Naoto
Robins, James A.
Vu, Huong T.
BIOPHYSICAL JOURNAL, 2024, 123 (03) : 362A - 363A

← 1 2 3 4 5 →