Preopening of the DNA base pairs

Kryachko, Eugene S.; Волков, С. Н.

doi:10.1002/qua.1040

Cited by 23 publications

(21 citation statements)

References 67 publications

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“…In the works [23,34] it is shown that the 'pre-opened' metastable state can be formed with the participation of water molecules (Fig.6b). It should be noted that our estimations for the difference in opening energies between A·T and G·C pairs for 'stretch' and 'stretch after opening' scenarios ( ∆E str and ∆E so ) are also appropriate for transition from the state where water is integrated to the external hydrogen bond (N 6 H•••O 4 for A·T ( Fig.6) and O 6 •••HN 4 for G·C) [34, fig.4].…”

Section: Discussionmentioning

confidence: 99%

“…So we consider that this transition does not require much energy and estimate the opening energy from the 'pre-opened' to the 'opened' state in this scenario. The existence of such a 'pre-opened' metastable state is shown in the works [23,34,35,37]. Let us make some qualitative estimations of the energy required for base pair transition from Watson-Crick state to the opened state for A·T and G·C base pairs.…”

Section: The Possible Pathways Of the Dna Unzipping Processmentioning

confidence: 99%

“…The estimations made in this section take into account only one degree of freedom: rotation of bases in a pair ('opening' pathway) or movement of bases relative to each Figure 6: Schematic representation of the adenine-thymine nucleic base pair in DNA macromolecule: a) Watson-Crick configuration [30]. The arrow shows the 'opening' pathway: the bases rotation around the axis passing through atoms C 1 perpendicular to the plane of the pair; b) 'pre-opened' A·T pair mediated by the water molecule [34].…”

Section: The Possible Pathways Of the Dna Unzipping Processmentioning

confidence: 99%

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Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments

Zdorevskyi

Волков

2018

Eur Biophys J

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Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom-atom potential function method. According to the first scenario, the base pairs transit into a 'preopened' metastable state and then fully open along the 'stretch' pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting. The second scenario is characterized by higher opening forces. In this case, the DNA base pairs open directly along the 'stretch' pathway. It follows from our calculations that, in this scenario, the enthalpy difference between the A[Formula: see text]T and G[Formula: see text]C base pairs is much higher than in the first case. The features of the first unzipping scenario show that it can play a key role during the process of DNA genetic information transfer in vivo. It follows from our study that a peculiarity of the second scenario is that it can be used for the development of faster methods for reading genetic information in vitro.

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Section: Discussionmentioning

confidence: 99%

Section: The Possible Pathways Of the Dna Unzipping Processmentioning

confidence: 99%

Section: The Possible Pathways Of the Dna Unzipping Processmentioning

confidence: 99%

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Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments

Zdorevskyi

Волков

2018

Eur Biophys J

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“…An opened base pair should provide high local flexibility [17], therefore it is a natural candidate to cause the formation of a kink holding the structure of a type 2 kink. The occurrence of the partially opened (preopened) configuratios of a base pair with possible binding of a water molecule to it [34,35] could be a reason to induce a type 2 kink in the double helix as well. Besides, the discovery of the formation of Hoogsteen base pairs in a linear DNA with a finite probability, which could provide high local flexibility as well [17,36], reveals another candidate to cause a type 2 kink.…”

Section: Kinks In the Kratky-porod Modelmentioning

confidence: 99%

Strong deformations of DNA: Effect on the persistence length

Simonov

2018

Eur. Phys. J. E

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Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.

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“…5,9,11 Essential structural and energetic features along with mechanistic pathways of many important chemical reactions can be studied using small gold clusters as catalytic models. [30][31][32][33][34][35][36] A unique feature of complexes between DNA bases and small gold clusters is the existence of nonconventional N-HÁ Á ÁAu hydrogen bonds. [27][28][29] The interaction of DNA with small gold clusters received special attention owing to its diverse applications in the field of electronics, sensors, drug delivery, chips, imaging, and more recently in heterogeneous catalysis.…”

Section: Introductionmentioning

confidence: 99%

Nucleobases tagged to gold nanoclusters cause a mechanistic crossover in the oxidation of CO

Rai

Ehara

2015

Phys. Chem. Chem. Phys.

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DNA is considered as a programmable building block for the assembly of nanomaterials that play a significant role in modern day nanotechnology and catalysis. In this work, density functional theory (DFT) is used to explore the possible application of complexes of DNA bases (adenine (A), thymine (T), guanine (G), and cytosine (C)) and their size expanded (x) counterparts with Au3 gold clusters as a model catalyst system for oxidation of CO to CO2. We investigate how the catalytic potential of the Au3 cluster is modulated on being tagged with the nuclebases. The CO oxidation can take place via the ER or the LH mechanism. On a pristine cluster, the LH pathway is thermodynamically favored. However, the CO oxidation reaction on the nucleobase tagged gold cluster is found to be more facile following the ER mechanism, with a significant reduction in the barrier height. The reduction in barrier height is attributed to the formation of additional hydrogen bonds between O2 and the polar sites of the attached base in the transition state. This indicates an interesting implication of tagging the cluster to a nucleobase resulting in a mechanistic crossover which is responsible for making nucleobase tagged gold clusters a better catalyst in comparison to pristine Au3 clusters. Our results indicate that nucleobase-gold cluster complexes open new avenues as efficient catalytic models having a wider range of technological applications.

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Preopening of the DNA base pairs

Cited by 23 publications

References 67 publications

Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments

Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments

Strong deformations of DNA: Effect on the persistence length

Nucleobases tagged to gold nanoclusters cause a mechanistic crossover in the oxidation of CO

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