ArticleMolecules (Basel, Switzerland)2021
Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 42 citations in OpenAlex.
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- A structural role for tryptophan in proteins, and the ubiquitous Trp CActa crystallographica. Section D, Structural biology · 2024Article
- Extraction of uranyl from spent nuclear fuel wastewater via complexation-a local vibrational mode study.Journal of molecular modeling · 2024Article
- Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson-Crick/Hoogsteen Base Pairs: A Computational Analysis.ACS omega · 2024Article
- Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair.ACS physical chemistry Au · 2024Article
- Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex inPhysical chemistry chemical physics : PCCP · 2024Article
- Harnessing non-Watson-Crick's base pairing to enhance CRISPR effectors cleavage activities and enable gene editing in mammalian cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids.International journal of molecular sciences · 2023Review
- Quantum Mechanical Assessment of Protein-Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory.International journal of molecular sciences · 2023Article
- Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy.Molecules (Basel, Switzerland) · 2022Article
- Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study.International journal of molecular sciences · 2022Article
- Uranium: The Nuclear Fuel Cycle and Beyond.International journal of molecular sciences · 2022Review
- On the formation of CN bonds in Titan's atmosphere-a unified reaction valley approach study.Journal of molecular modeling · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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