Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes
文献信息
Nivedita Dutta, Joanna Sarzynska, Indrajit Deb, Ansuman Lahiri
Pseudouridine (Ψ) and N1-methylpseudouridine (m1Ψ) are among the key modifications in the field of mRNA therapeutics and vaccine research. The accuracy of the design and development of therapeutic RNAs containing such modifications depends on the accuracy of the secondary structure prediction, which in turn depends on the nearest neighbor (NN) thermodynamic parameters for the standard and modified residues. Here, we propose a simple approach based on molecular dynamics simulations and linear interaction energy (LIE) approximation that is able to predict the NN free energy parameters for U–A, Ψ–A and m1Ψ–A pairs in reasonable agreement with the recent experimental reports. We report the NN thermodynamic parameters for different U, Ψ and m1Ψ base pairs, which might be helpful for a deeper understanding of the effect of these modifications in RNA. The predicted NN free energy parameters in this study are able to closely reproduce the folding free energies of duplexes containing internal Ψ for which the thermodynamic data were available. Additionally, we report the predicted folding free energies for the duplexes containing internal m1Ψ.
期刊推荐

New Journal of Chemistry

Current Opinion in Solid State & Materials Science

Crystallography Reports

Saudi Pharmaceutical Journal

Russian Journal of Bioorganic Chemistry

Nature Medicine

Organic Process Research & Development

Chemistry Education Research and Practice

Russian Journal of Coordination Chemistry

Russian Chemical Bulletin
相关文献
Gold and silver nanoparticles functionalized with known numbers of oligonucleotides per particle for DNA detection
Yang Chen, Jenny Aveyard, Robert Wilson
DOI: 10.1039/B411181H
The dynamic desorption of krypton from the zeolite chabazite
S. P. Cork, G. Cressey, R. H. Jones, S. J. Teat, V. L. Zholobenko
DOI: 10.1039/B410366C
Water-soluble supramolecular bowls formed by intra-clipping of resorcin[4]arene-based ligands with Pd(ii) ions
Seong Jin Park, Dong Mok Shin, Shigeru Sakamoto, Kentaro Yamaguchi, Young Keun Chung, Myoung Soo Lah
DOI: 10.1039/B212855A
From atactic to isotactic CO/p-methylstyrenecopolymer by proper modification of Pd(ii) catalysts bearing achiral α-diimines
Barbara Binotti, Carla Carfagna, Cristiano Zuccaccia, Alceo Macchioni
DOI: 10.1039/B411214H
Facile resolution of constrained geometry indenyl-phenoxide ligation
Luke E. Turner, Matthew G. Thorn, Phillip E. Fanwick, Ian P. Rothwell
DOI: 10.1039/B212724E
Palladium catalysed cyclisation–carbonylation of enynes to give cyclic γ,δ-unsaturated acids
Varinder K. Aggarwal, Mike Butters, Paul W. Davies
DOI: 10.1039/B300719G
Cyclopropyl fatty acids implicate a radical but not a cation as an intermediate in P450BM3-catalysed hydroxylations
Max J. Cryle, Julia M. U. Stuthe, Paul R. Ortiz de Montellano, James J. De Voss
DOI: 10.1039/B315911F
Synthesis of monodisperse chromium nanoparticles from the thermolysis of a Fischer carbene complex
Seung Uk Son, Youngjin Jang, Ki Youl Yoon, Changhua An, Yosun Hwang, Je-Geun Park, Han-Jin Noh, Jae-Young Kim, Jae-Hoon Park, Taeghwan Hyeon
DOI: 10.1039/B411656A
Phase-transfer alkylation reactions using microreactors
Masaharu Ueno, Hideaki Hisamoto, Takehiko Kitamori, Shū Kobayashi
DOI: 10.1039/B301638B
您可能还喜欢
如何处理含有8-氯咪唑并[1,2-A]吡嗪(CAS号:69214-33-1)的废料?
处理含有8-氯咪唑并[1,2-A]吡嗪的废料时,应首先将其收集并进行化学回收或降解。如果无法回收,需采用安全的化学处理方法,如中和、氧化还原或沉淀。处理过程中需...
Calhex 231 hydrochloride(CAS号:2387505-78-2)适用哪些法规指南?
Calhex 231 hydrochloride 需要遵循《全球化学品统一分类和标签制度》(GHS)的分类和标签要求,以及欧盟的《化学品注册、评估、授权和限制条...
11-Beta,17-alpha,21-三羟基-5-beta-孕烯-3,20-二酮(CAS号:1482-50-4)的物理化学性质是什么?
11-Beta,17-alpha,21-三羟基-5-beta-孕烯-3,20-二酮是一种无色结晶性粉末,分子量为372.45 g/mol。该化合物在水中的溶解度...
处理5-异丙基-1,3,4-恶二唑-2-羧酸(CAS号:944907-13-5)时应注意哪些实验室安全事项?
处理5-异丙基-1,3,4-恶二唑-2-羧酸时应注意以下安全事项:穿戴适当的个人防护装备,包括实验室外套、手套和护目镜;操作应在通风橱中进行,以减少吸入或接触有...
benzyl 3-bromopropanoate(CAS号:90841-55-7)安全吗?
Benzyl 3-bromopropanoate属于有毒物质,吸入、摄入或皮肤接触均可能对人体造成伤害。操作时应佩戴防护眼镜、口罩和手套,避免吸入蒸汽和直接接触...
什么是(R)-N-苄氧羰基-3,4-二氢-1H-异喹啉羧酸(CAS号:151004-88-5)?
(R)-N-苄氧羰基-3,4-二氢-1H-异喹啉羧酸是一种含有苄氧羰基和异喹啉环结构的化合物,分子式为C17H15NO3。它是一种有机化合物,具有一定的生物活性...
在合成中是否有1-苄基吡啶嗡-3-羧酸盐(CAS号:15990-43-9)的替代品?
可以考虑使用1-苄基吡啶-3-羧酸盐作为1-苄基吡啶嗡-3-羧酸盐的替代品。此外,还可以探索其他类似物,如1-苄基吡啶-3-氨基甲酸酯等。具体的替代品选择需根据...
(2,6-二甲基吡啶-3-基)甲醇(CAS号:582303-10-4)安全吗?
(2,6-二甲基吡啶-3-基)甲醇在使用时需注意安全,应避免吸入其蒸汽,接触皮肤和眼睛。操作应在通风良好的环境中进行,佩戴适当的个人防护装备。
5-溴-2-乙烯基吡啶(CAS号:226883-52-9)的物理化学性质是什么?
5-溴-2-乙烯基吡啶是一种有机化合物,外观为白色固体,具有良好的结晶性。分子量约为190.03 g/mol。它的溶解性在水中较差,但在有机溶剂如二氯甲烷、甲醇...
2-羟基-3-硝基-5-甲基吡啶(CAS号:7464-14-4)应用于哪些行业?
2-羟基-3-硝基-5-甲基吡啶主要应用于医药、聚合物和半导体行业。在医药领域,它可以用作合成其他药物的中间体。在聚合物领域,它可以作为功能性单体参与聚合反应,...
来源期刊
Physical Chemistry Chemical Physics

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.




