scholarly journals Investigation of DNA Breather Dynamics in A Model with Non-Local Inter-Site Interaction

2020 ◽  
Vol 15 (1) ◽  
pp. 93-105
Author(s):  
E.I. Geraskin ◽  
V.D. Lakhno ◽  
A.P. Chetverikov ◽  
A.S. Shigaev
Keyword(s):  
Stacking Interactions ◽  
Base Pairs ◽  
Non Local ◽  
Local Coupling ◽  
Nonlocal Nature

A variant of the Peyrard-Bishop-Dauxois model is proposed, which takes account of the partially delocalized nature of DNA stacking interactions. It is shown that the nonlocal nature of the inter-site potential can lead to an increase in the local cooperativity of the base pairs' opening an increasing in the number of simultaneously opening adjacent nucleotide pairs during the denaturation bubble's nucleation. The process of the formation and propagation of mobile breathers excited by the initial displacements of a number of nucleotide pairs has been studied. It is revealed that taking account of the non-local coupling in the Peyrard-Bishop-Dauxois model, while maintaining the remaining parameters of the model, leads to a decrease in the speed of the mobile breather and an increase in the probability of nucleation of the denaturation bubble.

scholarly journals Chimera states and the interplay between initial conditions and non-local coupling

2017 ◽  
Vol 27 (3) ◽  
pp. 033110 ◽  
Author(s):  
Peter Kalle ◽  
Jakub Sawicki ◽  
Anna Zakharova ◽  
Eckehard Schöll
Keyword(s):  
Initial Conditions ◽  
Chimera States ◽  
Non Local ◽  
Local Coupling

Non-Local Coupling and Partial Synchronization in Chaotic Systems

2006 ◽  
Vol 23 (4) ◽  
pp. 786-789 ◽  
Author(s):  
Ao Bin ◽  
Ma Xiao-Juan ◽  
Li Yun-Yun ◽  
Zheng Zhi-Gang
Keyword(s):  
Chaotic Systems ◽  
Partial Synchronization ◽  
Non Local ◽  
Local Coupling

scholarly journals Non-local coupling of two donor-bound electrons

2013 ◽  
Vol 15 (3) ◽  
pp. 033020 ◽  
Author(s):  
J Verduijn ◽  
R R Agundez ◽  
M Blaauboer ◽  
S Rogge
Keyword(s):  
Non Local ◽  
Local Coupling ◽  
Bound Electrons

scholarly journals Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

2010 ◽  
Vol 6 ◽  
Author(s):  
Daniel Lachmann ◽  
Sina Berndl ◽  
Otto S Wolfbeis ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Fluorescence Quenching ◽  
Nile Blue ◽  
Stacking Interactions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Postsynthetic Modification ◽  
Dna Models ◽  
Sensitive Tool ◽  
Opposite Chirality

The Nile Blue chromophore was incorporated into oligonucleotides using “click” chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV–vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.

scholarly journals A comprehensive survey on the nature of ring:ring nucleobase stacking interactions in RNA: occurrence, structural variability and classification of the associated contacts

2020 ◽  
Author(s):  
Ayush Jhunjhunwala ◽  
Zakir Ali ◽  
Sohini Bhattacharya ◽  
Antarip Halder ◽  
Abhijit Mitra ◽  
...  
Keyword(s):  
Classification System ◽  
Classification Scheme ◽  
Relative Orientation ◽  
Stacking Interactions ◽  
Automated Identification ◽  
Base Stacking ◽  
Base Pairs ◽  
Glycosidic Bonds ◽  
Comprehensive Survey

ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. Although the classification scheme proposed by Leontis and Westhof (RNA (2001), 7, 499) has been widely accepted for the annotation of RNA base pairs, the absence of an unambiguous classification system for base stacks appears to be a roadblock for exploring the stacking diversity in RNA. Here we provide an unambiguous and structurally-intuitive scheme for a geometry cum topology based classification of base stacking, where a stack is essentially classified in terms of the topology of the interacting nucleobase faces and the geometry described by the relative orientation of the glycosidic bonds. For heterodimeric stacks, this generates eight basic stacking geometric families, whereas for homodimeric stacks, this generates six of those. Further annotation in terms of the identity of the bases and the region of involvement of purines (5-membered, 6-membered or both rings), leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we also present an algorithm for automated identification of stacks in RNA crystal structures. Overall, the work described here is expected to greatly facilitate structure-based RNA research.

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