The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study

Literature Information

Publication Date 2016-09-22
DOI 10.1039/C6CP04617G
Impact Factor 3.676
Authors

Asmita Gupta, Manju Bansal


View Original

Abstract

Mechanical unfolding studies on Ribonucleic Acid (RNA) structures are a subject of tremendous interest as they shed light on the principles of higher order assembly of these structures. Pseudoknotting is one of the most elementary ways in which this higher order assembly is achieved as discrete secondary structural units in RNA are brought in close proximity to form a tertiary structure. Using steered molecular dynamics (SMD) simulations, we have studied the unfolding of five RNA pseudoknot structures that differ from each other either by base substitutions in helices or loops. Our SMD simulations reveal the manner in which a biologically functional RNA pseudoknot unfolds and the effect of changes in the primary structure on this unfolding pathway, providing necessary insights into the driving forces behind the functioning of these structures. We observed that an A → C mutation in the loop sequence makes the pseudoknot far more resistant against force induced disruption relative to its wild type structure. In contrast to this, a base-pair substitution GC → AU near the pseudoknot junction region renders it more vulnerable to this disruption. The quantitative estimation of differences in the unfolding paths was carried out using force extension curves, potential of mean force profiles, and the opening of different Watson–Crick and non-Watson–Crick interactions. The results provide a quantified view in which the unfolding paths of the small RNA structures can be used for investigating the programmability of RNA chains for designing RNA switches and aptamers as their biological folding and unfolding could be assessed and manipulated.

Related Literature

Femtosecond infrared spectroscopy of chlorophyll f-containing photosystem I

Noura Zamzam, Marius Kaucikas, Dennis J. Nürnberg, A. William Rutherford, Jasper J. van Thor

2018-12-10 Paper

DOI: 10.1039/C8CP05627G

Electric charge of nanopatterned silica surfaces

H. Gokberk Ozcelik, Murat Barisik

2019-03-13 Paper

DOI: 10.1039/C9CP00706G

Shape adaptation of quinine in cyclodextrin cavities: NMR studies

Jacek Wójcik, Andrzej Ejchart, Michał Nowakowski

2019-03-01 Paper

DOI: 10.1039/C9CP00590K

Hydrogen storage mechanism and diffusion in metal–organic frameworks

Mauro Boero

2019-01-03 Paper

DOI: 10.1039/C8CP07467D

Transition-metal dichalcogenides/Mg(OH)2 van der Waals heterostructures as promising water-splitting photocatalysts: a first-principles study

Yi Luo, Sake Wang, Kai Ren, Jyh-Pin Chou, Jin Yu, Zhengming Sun, Minglei Sun

2019-01-09 Paper

DOI: 10.1039/C8CP06960C

Ionic structure and transport properties of KF–NaF–AlF3 fused salt: a molecular dynamics study

Xiaojun Lv, Zexun Han, Hengxing Zhang, Qingsheng Liu, Jiangan Chen, Liangxing Jiang

2019-03-06 Paper

DOI: 10.1039/C9CP00377K

High-temperature shape memory loss in nitinol: a first principles study

Adebayo A. Adeleke, Yansun Yao

2019-03-21 Paper

DOI: 10.1039/C8CP07288D

Towards capturing cellular complexity: combining encapsulation and macromolecular crowding in a reverse micelle

Philipp Honegger, Othmar Steinhauser

2019-03-25 Paper

DOI: 10.1039/C9CP00053D

Using hydrogenated and perfluorinated gases to probe the interactions and structure of fluorinated ionic liquids

Luiz Fernando Lepre, Laure Pison, Ines Otero, Arnaud Gautier, Julien Dévemy, Pascale Husson, Agilio A. H. Pádua, Margarida Costa Gomes

2019-04-09 Paper

DOI: 10.1039/C9CP00593E

Unraveling the molecular mechanisms of color expression in anthocyanins

Luca Grisanti, Sara Laporte, Marco Micciarelli, Marta Rosa, Rebecca J. Robbins, Tom Collins, Alessandra Magistrato

2019-03-18 Paper

DOI: 10.1039/C9CP00747D

You might also like

Compound Q&A

Are there alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3848-36-0) in synthesis?

When considering alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3...

3848-36-01-(4-Chlorophenyl)-N...
Compound Q&A

How is 3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole (CAS: 419553-16-5) typically synthesized?

3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole is synthesized through a m...

419553-16-53-(4-Bromophenyl)-5-...
Compound Q&A

How is 5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS: 1639220-19-1) typically synthesized?

5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS...

1639220-19-15-Chloro-2-(4-chloro...
Compound Q&A

What industries use 2-Chloro-4-(difluoromethoxy)pyridine (CAS: 1206978-15-5)?

2-Chloro-4-(difluoromethoxy)pyridine is used in the pharmaceutical industry for ...

1206978-15-52-Chloro-4-(difluoro...
Compound Q&A

What regulatory guidelines apply to 3-Chloro-6-methylpyridazine (CAS: 1121-79-5)?

3-Chloro-6-methylpyridazine (CAS: 1121-79-5) is classified under the Globally Ha...

1121-79-53-Chloro-6-methylpyr...
Compound Q&A

Are there alternatives to Methyl 4,5-dimethyl-2-nitrobenzoate in synthesis?

Several alternatives can be used in the synthesis of Methyl 4,5-dimethyl-2-nitro...

90922-74-0Methyl 4,5-dimethyl-...
Compound Q&A

Are there alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde in synthesis?

Alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde include other acry...

63405-68-5(2E,2'E)-3,3'-(1,4-P...
Compound Q&A

What is 3-Amino-5-chloropyridin-2-ol hydrochloride (CAS: 1261906-29-9)?

3-Amino-5-chloropyridin-2-ol hydrochloride is an organic compound with the CAS n...

1261906-29-93-Amino-5-chloropyri...
Compound Q&A

What precautions should be taken when handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one (CAS: 1092349-93-3)?

When handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one, it is essential to wear...

1092349-93-36,7-Difluoro-2,3-dih...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.