A TDDFT Study of the Optical Response of DNA Bases, Base Pairs, and Their Tautomers in the Gas Phase

2005 ◽  
Vol 109 (10) ◽  
pp. 2373-2380 ◽  
Author(s):  
Argyrios Tsolakidis ◽  
Efthimios Kaxiras
Keyword(s):  
Gas Phase ◽  
Optical Response ◽  
Dna Bases ◽  
Base Pairs

scholarly journals A ‘bottom up’, ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs

2016 ◽  
Vol 18 (30) ◽  
pp. 20007-20027 ◽  
Author(s):  
Barbara Marchetti ◽  
Tolga N. V. Karsili ◽  
Michael N. R. Ashfold ◽  
Wolfgang Domcke
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Radiative Decay ◽  
Computational Study ◽  
Computational Approach ◽  
Dna Bases ◽  
Base Pairs ◽  
Bottom Up ◽  
Photophysical Processes ◽  
Uv Excitation

A systematic computational study of non-radiative decay pathways following UV excitation of selected heterocycles, DNA bases, nucleosides and base-pairs in the gas phase.

scholarly journals Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik
Keyword(s):  
Base Pair ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Dna Bases ◽  
Halogen Bonds ◽  
Base Pairs ◽  
Rich Diversity ◽  
Different Types ◽  
Guanine Base ◽  
The Stability

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

scholarly journals The Uracil DNA Glycosylase UdgB of Mycobacterium smegmatis Protects the Organism from the Mutagenic Effects of Cytosine and Adenine Deamination

2009 ◽  
Vol 191 (20) ◽  
pp. 6312-6319 ◽  
Author(s):  
Roger M. Wanner ◽  
Dennis Castor ◽  
Carolin Güthlein ◽  
Erik C. Böttger ◽  
Burkhard Springer ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
High Efficiency ◽  
Genetic Manipulation ◽  
Dna Bases ◽  
Dna Glycosylase ◽  
Base Pairs ◽  
Uracil Dna Glycosylase ◽  
Extreme Habitats ◽  
Mutagenic Effects

ABSTRACT Spontaneous hydrolytic deamination of DNA bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats. Cytosine is readily deaminated to uracil, which base pairs with adenine during replication, and most organisms encode at least one uracil DNA glycosylase (UDG) that removes this aberrant base from DNA with high efficiency. Adenine deaminates to hypoxanthine approximately 10-fold less efficiently, and its removal from DNA in vivo has to date been reported to be mediated solely by alkyladenine DNA glycosylase. We previously showed that UdgB from Pyrobaculum aerophilum, a hyperthermophilic crenarchaeon, can excise hypoxanthine from oligonucleotide substrates, but as this organism is not amenable to genetic manipulation, we were unable to ascertain that the enzyme also has this role in vivo. In the present study, we show that UdgB from Mycobacterium smegmatis protects this organism against mutagenesis associated with deamination of both cytosine and adenine. Together with Ung-type uracil glycosylase, M. smegmatis UdgB also helps attenuate the cytotoxicity of the antimicrobial agent 5-fluorouracil.

scholarly journals Optical Response of Gas-Phase Atoms at Less thanλ/80from a Dielectric Surface

2014 ◽  
Vol 112 (25) ◽  
Author(s):  
K. A. Whittaker ◽  
J. Keaveney ◽  
I. G. Hughes ◽  
A. Sargsyan ◽  
D. Sarkisyan ◽  
...  
Keyword(s):  
Gas Phase ◽  
Optical Response ◽  
Dielectric Surface

Anharmonic Vibrational Signatures of DNA Bases and WatsonCrick Base Pairs

2009 ◽  
Vol 22 (6) ◽  
pp. 563-570 ◽  
Author(s):  
Gui-xiu Wang ◽  
Xiao-yan Ma ◽  
Jian-ping Wang
Keyword(s):  
Dna Bases ◽  
Base Pairs

scholarly journals The DNA Barcoding of Several Commercial Fish from Simeulue Islands Coast of Aceh Using Cytochrome Oxidase Sub Unit I (COI) Gene Marker

2019 ◽  
Vol 1 (1) ◽  
pp. 62-70
Author(s):  
Edwarsyah Edwarsyah ◽  
Muhammad Nasir ◽  
Muhammad Banda Selamat
Keyword(s):  
Dna Barcoding ◽  
Species Level ◽  
Dna Bases ◽  
Coi Gene ◽  
Gene Marker ◽  
Base Pairs ◽  
Commercial Fish ◽  
Morphological Approach ◽  
Mitochodrial Dna ◽  
The Right

Simeulue is a cluster of islands that rich of commercial fisheries in Aceh waters. Management of the fisheries products is highly related to species identification in order to ascertain the appropriate steps to manage the resources sustainably. Identification using DNA barcoding tools is the right answer for the problem that have not been able to be resolved even by morphological approach. Some of 11 individual samples were taken from 6 sampling points based on lobster’s catchment and cultivation areas. All of the samples were identified using COI mitochodrial DNA resulting 6 species including Scomber scombus, Scomberomorus plurilineatus, Octopus cyanea, Taeniura Lymna, Sympterygia bonapartii and Panulirus versicolor. The DNA bases were aligned using MEGA application and Neigbour- Joining method, Kimura 2 parameters resulting a 690 base pairs nucleotides. Reconstruction of philogenetic tree shows that the species of Simeulue were conjoined into one clade with the sequences downloaded from genebank. It shows that those species were closely related genetically indicating by the bootstrap value of Scomber scombus (100), Scomberomorus plurilineatus (100), Octopus cyanea (100). The results of the study shows that the DNA barcoding tools can explicate not only the identification up to the species level but also the genetic relationship that can be seen from the interspecies bases composition.

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