A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G–C base pairs

2020 ◽  
Vol 22 (20) ◽  
pp. 11546-11557 ◽  
Author(s):  
Ruodi Cheng ◽  
Jonathan Martens ◽  
Travis D. Fridgen
Keyword(s):  
Alkali Metal ◽  
Computational Methods ◽  
Computational Study ◽  
Base Pairs ◽  
Irmpd Spectroscopy ◽  
Structures And Properties

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M+, where M+ = Li+, Na+, K+, Rb+, Cs+ as well as the protonated complex, (9eG:1mC)H+, have been studied using a combination of IRMPD spectroscopy and computational methods.

Hydrogen bonding in alkali metal cation-bound i-motif-like dimers of 1-methyl cytosine: an IRMPD spectroscopic and computational study

2019 ◽  
Vol 21 (21) ◽  
pp. 11103-11110 ◽  
Author(s):  
Ruodi Cheng ◽  
Estelle Loire ◽  
Travis D. Fridgen
Keyword(s):  
Hydrogen Bonding ◽  
Alkali Metal ◽  
Gas Phase ◽  
Vibrational Spectroscopy ◽  
Computational Methods ◽  
Metal Cation ◽  
Computational Study ◽  
Alkali Metal Cation ◽  
Alkali Metal Cations ◽  
Methyl Cytosine

The structures of alkali metal cation bound 1-methylcytosine (1-mCyt) dimers were explored using vibrational spectroscopy in the gas phase and by computational methods. A transition from structures absent of hydrogen bonding for the light alkali metal cations to those with predominant hydrogen bonding for the larger cations was observed.

scholarly journals Capture of a Transition State Using Molecular Dynamics: Creation of an Intercalation Site in dsDNA with Ethidium Cation

2010 ◽  
Vol 2010 ◽  
pp. 1-4 ◽  
Author(s):  
Regina R. Monaco
Keyword(s):  
External Surface ◽  
Computational Study ◽  
Helical Axis ◽  
Base Pairs ◽  
Bond Rotation ◽  
Double Stranded Dna ◽  
Dna Backbone ◽  
Interaction Measure ◽  
The Creation ◽  
A Site

The mechanism of intercalation and the ability of double stranded DNA (dsDNA) to accommodate a variety of ligands in this manner has been well studied. Proposed mechanistic steps along this pathway for the classical intercalator ethidium have been discussed in the literature. Some previous studies indicate that the creation of an intercalation site may occur spontaneously, with the energy for this interaction arising either from solvent collisions or soliton propagation along the helical axis. A subsequent 1D diffusional search by the ligand along the helical axis of the DNA will allow the ligand entry to this intercalation site from its external, electrostatically stabilized position. Other mechanistic studies show that ethidium cation participates in the creation of the site, as a ligand interacting closely with the external surface of the DNA can cause unfavorable steric interactions depending on the ligands' orientation, which are relaxed during the creation of an intercalation site. Briefly, such a site is created by the lengthening of the DNA molecule via bond rotation between the sugars and phosphates along the DNA backbone, causing an unwinding of the dsDNA itself and separation between the adjacent base pairs local to the position of the ligand, which becomes the intercalation site. Previous experimental measurements of this interaction measure the enthalpic cost of this part of the mechanism to be about −8 kcal/mol. This paper reports the observation, during a computational study, of the spontaneous opening of an intercalation site in response to the presence of a single ethidium cation molecule in an externally bound configuration. The concerted motions between this ligand and the host, a dsDNA decamer, are clear. The dsDNA decamer AGGATGCCTG was studied; the central site was the intercalation site.

Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study

2017 ◽  
Vol 19 (25) ◽  
pp. 16638-16649 ◽  
Author(s):  
Aurellia Galliot ◽  
Adrià Gil ◽  
Maria José Calhorda
Keyword(s):  
Driving Force ◽  
Computational Study ◽  
Solvation Energy ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.

The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N–H and O–H stretching region and computational methods

2014 ◽  
Vol 16 (48) ◽  
pp. 26855-26863 ◽  
Author(s):  
Yasaman Jami Alahmadi ◽  
Ameneh Gholami ◽  
Travis D. Fridgen
Keyword(s):  
Computational Methods ◽  
Canonical Structure ◽  
Irmpd Spectroscopy

Determination of the zwitterionic or canonical structure of proline in protonated and sodiated proline dimers.

The effect of the aliphatic carboxylate linkers on the electronic structures, chemical bonding and optical properties of the uranium-based metal–organic frameworks

RSC Advances ◽  
2015 ◽  
Vol 5 (34) ◽  
pp. 26735-26748 ◽  
Author(s):  
Saumitra Saha ◽  
Udo Becker
Keyword(s):  
Optical Properties ◽  
Detailed Analysis ◽  
Computational Methods ◽  
Chemical Bonding ◽  
Electronic Structures ◽  
Computational Study ◽  
Metal Organic Frameworks ◽  
Metal Organic ◽  
First Time

A series of uranyl containing aliphatic dicarboxylate structures is studied using computational methods. Our computational study provides a detailed analysis of these MOFs and explores the effect of linkers on their properties for the first time.

scholarly journals Importance of base-pair opening for mismatch recognition

2020 ◽  
Vol 48 (20) ◽  
pp. 11322-11334
Author(s):  
Tomáš Bouchal ◽  
Ivo Durník ◽  
Viktor Illík ◽  
Kamila Réblová ◽  
Petr Kulhánek
Keyword(s):  
Base Pair ◽  
Computational Study ◽  
Minor Groove ◽  
Base Pairs ◽  
Theoretical Support ◽  
Molecular Pattern ◽  
Anti Cancer ◽  
Mismatch Recognition ◽  
Base Pair Opening

Abstract Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.

Interaction of nucleic acid bases and Watson–Crick base pairs with fullerene: Computational study

2010 ◽  
Vol 493 (1-3) ◽  
pp. 130-134 ◽  
Author(s):  
Manoj K. Shukla ◽  
Madan Dubey ◽  
Eugene Zakar ◽  
Raju Namburu ◽  
Jerzy Leszczynski
Keyword(s):  
Nucleic Acid ◽  
Computational Study ◽  
Nucleic Acid Bases ◽  
Base Pairs
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