scholarly journals Effects of Stability of Base Pairs Containing an Oxazolone on DNA Elongation

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Masayo Suzuki ◽  
Kazuya Ohtsuki ◽  
Katsuhito Kino ◽  
Teruhiko Kobayashi ◽  
Masayuki Morikawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Oxidative Damage ◽  
Ab Initio ◽  
Base Pair ◽  
Thermal Denaturation ◽  
Primer Extension ◽  
Base Pairs ◽  
Nucleotide Incorporation ◽  
The Stability

The nucleoside 2,2,4-triamino-5(2H)-oxazolone (Oz) can result from oxidative damage to guanine residues in DNA. Despite differences among the three polymerases (Polβ, KF exo−, and Polη) regarding nucleotide incorporation patterns opposite Oz, all three polymerases can incorporate guanine opposite Oz. Based onab initiocalculations, we proposed a structure for a stable Oz:G base pair. Here, to assess the stability of each Oz-containing base pair (Oz:G, Oz:A, Oz:C, and Oz:T) upon DNA replication, we determined the efficiency of Polβ-, KF exo−-, or Polη-catalyzed primer extension beyond each base pair. With each polymerase, extension beyond Oz:G was more efficient than that beyond Oz:A, Oz:C, or Oz:T. Moreover, thermal denaturation studies revealed that theTmvalue for the duplex containing Oz:G was significantly higher than those obtained for duplexes containing Oz:A, Oz:C, or Oz:T. Therefore, the results fromab initiocalculations along with those from DNA replication assays and thermal denaturation experiments supported the conclusion that Oz:G is the most stable of the Oz-containing base pairs.

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 Crystallographic evidence of Watson–Crick connectivity in the base pair of anionic adenine with thymine

2020 ◽  
Vol 117 (31) ◽  
pp. 18224-18230
Author(s):  
Manish Kumar Mishra ◽  
Steven P. Kelley ◽  
Volodymyr Smetana ◽  
David A. Dixon ◽  
Ashley S. McNeill ◽  
...  
Keyword(s):  
Gas Phase ◽  
Base Pair ◽  
Phase Reaction ◽  
Base Pairs ◽  
Gas Phase Reaction ◽  
Neutral Base ◽  
The Stability ◽  
Structure Calculations ◽  
Insight Into ◽  
Stable Formation

Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N4444]+) or tetrabutylphosphonium ([P4444]+) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N4444][Ad]·2H2O, and thymine, [P4444][Thy]·2H2O, as well as the double salt cocrystal, [P4444]2[Ad][Thy]·3H2O·2HThy. The cocrystal includes the anionic [Ad−(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson–Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.

QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE

2008 ◽  
Vol 07 (03) ◽  
pp. 317-329 ◽  
Author(s):  
SIAVASH RIAHI ◽  
MOHAMMAD REZA GANJALI ◽  
PARVIZ NOROUZI
Keyword(s):  
Base Pair ◽  
Dft Method ◽  
Base Pairs ◽  
Dispersion Energy ◽  
Charge Delocalization ◽  
Dna Base ◽  
Quantum Mechanical Description ◽  
London Dispersion ◽  
Dna Base Pair ◽  
The Stability

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

scholarly journals Insights into I-motif stabilization by high resolution primer extension assays: Its strengths and limitations

2022 ◽  
Author(s):  
Jan Jamroskovic ◽  
Marco Deiana ◽  
Nasim Sabouri
Keyword(s):  
High Resolution ◽  
Small Molecules ◽  
Primer Extension ◽  
Base Pairs ◽  
Promising Candidate ◽  
Experimental Conditions ◽  
Biologically Relevant ◽  
Wide Range ◽  
G Quadruplex ◽  
The Stability

Cytosine-rich DNA can fold into four-stranded intercalated structures, i-motif (iM), in acidic pH and require hemi-protonated C:C+ base pairs to form. However, its formation and stability rely on many other factors that are not yet fully understood. In here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability in a wide range of experimental conditions. By using high resolution primer extension assays, circular dichroism and absorption spectroscopies, we demonstrate that the stability of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature, and demonstrated that the G-quadruplex-specific molecule, CX-5461, is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding biological roles of iMs and their potential as therapeutic targets.

scholarly journals The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
William H. Gmeiner ◽  
Freddie Salsbury ◽  
Chris M. Olsen ◽  
Luis A. Marky
Keyword(s):  
Base Pair ◽  
Cleavage Site ◽  
Nucleoside Analogs ◽  
Dna Duplex ◽  
Base Pairs ◽  
Topoisomerase 1 ◽  
Mismatched Base Pair ◽  
The Stability ◽  
Dynamics Simulations ◽  
Dna Complex

Topoisomerase 1 (Top1) enzymes regulate DNA superhelicity by forming covalent cleavage complexes that undergo controlled rotation. Substitution of nucleoside analogs at the +1 position of the DNA duplex relative to the Top1 cleavage site inhibits DNA religation. The reduced efficiency for Top1-mediated religation contributes to the anticancer activity of widely used anticancer drugs including fluoropyrimidines and gemcitabine. In the present study, we report that mismatched base pairs at the +1 position destabilize the duplex DNA components for a model Top1 cleavage complex formation even though one duplex component does not directly include a mismatched base pair. Molecular dynamics simulations reveal G-dU and G-FdU mismatched base pairs, but not a G-T mismatched base pair, increase flexibility at the Top1 cleavage site, and affect coupling between the regions required for the religation reaction to occur. These results demonstrate that substitution of dT analogs into the +1 position of the non-scissile strand alters the stability and flexibility of DNA contributing to the reduced efficiency for Top1-mediated DNA religation. These effects are inherent in the DNA duplex and do not require formation of the Top1:DNA complex. These results provide a biophysical rationale for the inhibition of Top1-mediated DNA religation by nucleotide analog substitution.

scholarly journals Thermal denaturation in acidic solutions of double-helical ribonucleic acid from virus-like particles found in Penicillium chrysogenum. A spectrophotometric study

1971 ◽  
Vol 125 (2) ◽  
pp. 655-665 ◽  
Author(s):  
R. A. Cox ◽  
K. Kanagalingam ◽  
Elisabeth Sutherland
Keyword(s):  
Base Pair ◽  
Penicillium Chrysogenum ◽  
Sodium Phosphate ◽  
Thermal Denaturation ◽  
Spectrophotometric Study ◽  
Base Pairs ◽  
Native Form ◽  
Acidic Solutions ◽  
Ph Values ◽  
Sodium Phosphate Buffer

1. Two species of double-helical RNA isolated from mycelium of Penicillium chrysogenum were titrated with acid at 25°C and 95°C (solvent 0.1m-sodium phosphate buffer). At 25°C denaturation occurred at about pH3. At 95°C in the denatured form cytosine residues titrated as a simple monobasic acid of pK3.9 compared with pK≃2.5 for the native form at 25°C. 2. On thermal denaturation in neutral and acidic solutions one species of RNA (38% rG·rC) ‘melted’ in three distinct stages, equivalent to a mixture of three species, namely one of about 25% rG·rC, another of about 33% rG·rC and a third of about 46% rG·rC: the relative proportions were 0.25:0.35:0.40. 3. On thermal denaturation in acidic solutions the increase in the fraction of ionized cytosine residues concomitant with the ‘melting’ of rG·rC base pair also affects the spectrum especially at 280nm and serves to enhance the contribution of rG·rC base pairs at this wavelength. The increment in ε(P) at 280nm on ‘melting’ an rG·rC base pair approaches 53501·mol−1·cm−1 depending on pH, compared with 33501·mol−1·cm−1 at pH7. In contrast ε(P) at 280nm is scarcely affected by ‘melting’ rA·rU base pairs or by the protonization of adenine residues. 4. Changes in the spectrum of Escherichia coli rRNA on denaturation in acidic solutions were studied to yield the mole fractions of rA·rU and rG·rC base pairs ‘melting’ at particular pH values.

Ab Initio and Density Functional Studies of Substituent Effects of an A−U Base Pair on the Stability of Hydrogen Bonding

1999 ◽  
Vol 103 (42) ◽  
pp. 8516-8523 ◽  
Author(s):  
Shun-ichi Kawahara ◽  
Takeshi Wada ◽  
Susumu Kawauchi ◽  
Tadafumi Uchimaru ◽  
Mitsuo Sekine
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Base Pair ◽  
Density Functional ◽  
Substituent Effects ◽  
Functional Studies ◽  
The Stability

scholarly journals Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 387 ◽  
Author(s):  
Ye Teng ◽  
Hisae Tateishi-Karimata ◽  
Tatsuya Ohyama ◽  
Naoki Sugimoto
Keyword(s):  
Base Pair ◽  
Potassium Concentration ◽  
Quantitative Information ◽  
Molecular Crowding ◽  
Dilute Solution ◽  
Base Pairs ◽  
Dna Structures ◽  
Dilute Aqueous Solutions ◽  
K Concentration ◽  
The Stability

The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different C+*G-C triplet content (*: Hoogsteen base pair; - : Watson–Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K+ concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of C+*G-C triplets increased. Under molecular crowding conditions, Watson–Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (≤1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the C+*G-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K+ concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.

scholarly journals Role of pH in The Stability of Cytosine-Cytosine Mismatch and Canonical AT & GC Base Pairs Mediated With Silver Ion: A DFT Study

2021 ◽  
Author(s):  
Surjit Bhai ◽  
Bishwajit Ganguly
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acids ◽  
Base Pair ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Aim Analysis ◽  
C Complex ◽  
The Stability ◽  
Ph Range

Abstract Metallo-nucleic acids have been investigated for their applications in the field of nanodevices and genetic expansion. The cytosine-Ag+-cytosine mismatch base pair interactions and their stability in nucleic acids have attracted the attention of chemists. We report a systematic study of canonical, mismatch, Ag+ mediated system with CC, AT, and GC base pairs computationally. The stability of such mismatch base pairs is dependent on the pH range ~5 to 9 and the duplexes beyond this range are unstable. The DFT calculations performed with the model DNA duplexes comprising of such mismatch pairs reveal the stability trend while varying the pH conditions. The stability of canonical Watson-Crick ATGC base pairs was compared with the CCAT and CCGC mismatch base pairs and the calculated results at B3LYP-D3/6-31G* level of theory in the aqueous phase suggest that the base stacking and hydrogen bonding are well maintained in the former case, however, the larger perturbations in the geometry are observed with the mispair and relatively unstable. The calculated binding energy at B3LYP/6-31G* level of theory of ATGC is energetically more stable (~15 kcal/mol) than the mismatch base pairs. The Ag+ mediated mismatch base pairs i.e., C_CAT and C_CGC examined at the same level of theory suggest that the CC mismatch base pairs complexed with proper alignment to the Ag+ ion and the AT and GC bases maintained the hydrogen bonding interactions. The mismatched base pair duplex systems i.e., C_CAT and C_CGC are structurally similar to the canonical Watson-Crick base pairs and energetically stable by ~40 and ~50 kcal/mol compared to the canonical ATGC base pairs. The experimental report on the thermal transition profile in 5’-(A)10C(A)10-3’ and 5’ (T)10C(T)10-3’ duplexes showed remarkable stability and corroborate the calculated results.[1] The stability of Ag+ mediated mismatch bases at the higher pH 9 was also examined and the nucleobases such as guanine and thymine would be deprotonated under this condition. The calculated results suggest that the CCA_T and CCG_C duplexes are largely distorted with the complexation of Ag+ with the AT and GC base pairs and would in turn denature the duplex. The AIM analysis performed at B3LYP-D3/6-31G* level of theory for all the studied Ag+ mediated complexes reveals that the Ag+ interaction with the corresponding nucleobases was electrostatic in nature. The role of pH in governing the stability of C-Ag+-C complex formation in mismatch base nucleic acids is crucial for their application of genetic expansion and nucleic acid-based nanodevices.

Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair

1999 ◽  
Vol 4 (5) ◽  
pp. 537-545 ◽  
Author(s):  
Jiří Šponer ◽  
Michal Sabat ◽  
Jaroslav V. Burda ◽  
Jerzy Leszczynski ◽  
Pavel Hobza ◽  
...  
Keyword(s):  
Metal Ions ◽  
Ab Initio ◽  
Base Pair ◽  
Ab Initio Study ◽  
Base Pairs ◽  
Complementary Dna ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Adenine Base
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