Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet
Literature Information
Wenjuan Wang, Xiehuang Sheng, Shaolong Zhang, Fang Huang, Chuanzhi Sun, Jianbiao Liu, Dezhan Chen
The addition of the unnatural P:Z base pair to the four naturally occurring DNA bases expands the genetic alphabet and yields an artificially expanded genetic information system (AEGIS). Herein, the structural feature of oligonucleotides containing a novel unnatural P:Z base pair is characterized using both molecular dynamics and quantum chemistry. The results show that the incorporation of the novel artificial base pair (P:Z) preserves the global conformational feature of duplex DNA except for some local structures. The Z-nitro group imparts new properties to the groove width, which widens the major groove. The unnatural oligonucleotides containing mismatched base pairs exhibit low stability. This ensures efficient and high-fidelity replication. In general, the incorporation of the P:Z pair strengthens the stability of the corresponding DNA duplex. The calculated results also show that the thermostability originates from both hydrogen interaction and stacking interaction. The Z-nitro group plays an important role in enhancing the stability of the H-bonds and stacking strength of the P:Z pair. Overall, the present results provide theoretical insights in the exploration of artificially expanded genetic information systems.
Related Literature
A critical comparison of neural network potentials for molecular reaction dynamics with exact permutation symmetry
Kaisheng Song, Jörg Behler
DOI: 10.1039/C8CP06919K
Unraveling the molecular conformations of a single ruthenium complex adsorbed on the Ag(111) surface by calculations
Youness Benjalal, Jacques Bonvoisin, Xavier Bouju
DOI: 10.1039/C9CP01244C
Surface termination of MgB2 unveiled by a combination of adsorption experiments and theoretical calculations
Barbora Prudilová, Eva Otyepková, Jindřich Fanfrlík, Drahomír Hnyk, Josef Holub, Martin Petr, Jan Filip, Klára Čépe, Petr Lazar, Michal Otyepka
DOI: 10.1039/C9CP00771G
A deconvolution protocol of the mechanical relaxation spectrum to identify and quantify individual polymer feature contributions to self-healing
Vincenzo Montano, Stephen J. Picken, Sybrand van der Zwaag, Santiago J. Garcia
DOI: 10.1039/C9CP00417C
A new insight into the SO2 adsorption behavior of oxidized carbon materials using model adsorbents and DFT calculations
Xinxin Pi, Fei Sun, Jihui Gao, Zhibin Qu, Ani Wang, Zhipeng Qie, Lijie Wang, Hui Liu
DOI: 10.1039/C8CP07782G
Imaging inelastic scattering of CO with argon: polarization dependent differential cross sections
Zhong-Fa Sun, Chandan K. Bishwakarma, Lei Song, Ad van der Avoird, Marc C. van Hemert, Arthur G. Suits, George C. McBane, David H. Parker
DOI: 10.1039/C9CP00876D
An accurate measurement of the dipole orientation in various organic semiconductor films using photoluminescence exciton decay analysis
Ik Jang Ko, Hyuna Lee, Jin Hwan Park, Gyeong Woo Kim, Raju Lampande, Ramchandra Pode, Jang Hyuk Kwon
DOI: 10.1039/C9CP00965E
Order parameters, orientational distribution functions and heliconical tilt angles of oligomeric liquid crystals
Richard J. Mandle, John W. Goodby
DOI: 10.1039/C9CP00736A
Ionic conductivity of deep eutectic solvents: the role of orientational dynamics and glassy freezing
Daniel Reuter, Catharina Binder, Peter Lunkenheimer, Alois Loidl
DOI: 10.1039/C9CP00742C
You might also like
How is Ethyl 4-chlorothieno[2,3-b]pyridine-5-carboxylate (CAS: 59713-58-5) typically synthesized?
Ethyl 4-chlorothieno[2,3-b]pyridine-5-carboxylate (CAS: 59713-58-5) can be synth...
What regulatory guidelines apply to 5-Methyl-1H-indole-3-carbaldehyde (CAS: 52562-50-2)?
5-Methyl-1H-indole-3-carbaldehyde (CAS: 52562-50-2) is subject to various regula...
What are the physical and chemical properties of (1,3-Dimethyl-2,4-dioxo-1,2,3,4-tetrahydro-5-pyrimidinyl)boronic acid (CAS: 223418-73-3)?
(1,3-Dimethyl-2,4-dioxo-1,2,3,4-tetrahydro-5-pyrimidinyl)boronic acid is a white...
How should waste containing Sulfocostunolide A (CAS: 1016983-51-9) be handled?
Waste containing Sulfocostunolide A (CAS: 1016983-51-9) should be handled with c...
What precautions should be taken when handling Murraxocin (CAS: 88478-44-8)?
When handling Murraxocin (CAS: 88478-44-8), ensure proper personal protective eq...
What are the physical and chemical properties of Formvar (CAS: 63148-64-1)?
Formvar (CAS: 63148-64-1) is an alkyd resin characterized by a high molecular we...
Is (S)-4-benzyl-2-((benzyloxy)methyl)morpholine (CAS: 205242-66-6) safe?
(S)-4-benzyl-2-((benzyloxy)methyl)morpholine is generally safe when handled with...
What industries use Methyl 1-(5-bromo-2-pyrimidinyl)cyclopropanecarboxylate (CAS: 1447607-69-3)?
Methyl 1-(5-bromo-2-pyrimidinyl)cyclopropanecarboxylate (CAS: 1447607-69-3) is p...
Is 2-Methyl-1-phenyl-1-propanamine hydrochloride (CAS: 24290-47-9) safe?
2-Methyl-1-phenyl-1-propanamine hydrochloride (CAS: 24290-47-9) is generally con...
How is 3-(4-Bromophenyl)-2-methylpropanoic acid (CAS: 66735-01-1) typically synthesized?
3-(4-Bromophenyl)-2-methylpropanoic acid is synthesized through a multi-step pro...
Source Journal
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.













![2-(Methylsulfonyl)-2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole structure 2-(Methylsulfonyl)-2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole structure](https://static.chemtradehub.com/structs/122/1226781-80-1-09d5.webp)
