scholarly journals Bending and Base-Stacking Interactions in Double-Stranded DNA

1999 ◽  
Vol 82 (22) ◽  
pp. 4560-4563 ◽  
Author(s):  
Zhou Haijun ◽  
Zhang Yang ◽  
Ou-Yang Zhong-can
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40255-40262 ◽  
Author(s):  
Shikhar Tyagi ◽  
Sarika Saxena ◽  
Nikita Kundu ◽  
Taniya Sharma ◽  
Amlan Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synthetic Peptide ◽  
High Selectivity ◽  
Selective Recognition ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna ◽  
G Quadruplex ◽  
Guanine Base

A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.

BENDING AND BASE-STACKING INTERACTIONS IN DOUBLE-STRANDED DNA

APPC 2000 ◽  
2001 ◽  
Author(s):  
HAIJUN ZHOU ◽  
YANG ZHANG ◽  
ZHONG-CAN OU-YANG
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Distributed chaos in DNA

2018 ◽  
Author(s):  
A. Bershadskii
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequence ◽  
Kam Theory ◽  
Translational Symmetry ◽  
Stacking Interactions ◽  
Dna Dynamics ◽  
Base Stacking ◽  
Genetic Sequencing ◽  
Model Plant ◽  
Human Genes

It is shown that distributed chaos, generated by Hamiltonian DNA dynamics with spontaneously broken time translational symmetry, imprints itself on the DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and mapping) and of the NRXN1 and BRCA2 human genes (as an example). The base-stacking interactions in the DNA duplex, degenerate codon groups and a relation to the KAM theory have been discussed in this context.

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.

Experimental and Numerical Studies on B-DNA Overstretching Transition in Presence of Sodium Ions at Physiological Temperature

2007 ◽  
Vol 121-123 ◽  
pp. 1093-1096 ◽  
Author(s):  
Hong Xia Fu ◽  
Chan Ghee Koh ◽  
Hu Chen ◽  
Chwee Teck Lim
Keyword(s):  
Optical Tweezers ◽  
Electrostatic Interactions ◽  
Electrostatic Energy ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Physiological Temperature ◽  
Dna Molecule ◽  
Metropolis Monte Carlo ◽  
Dna Double Helix ◽  
Transition Force

In this paper, the effects of Na+ concentration on the overstretching transition of B-DNA molecule at physiological temperature are studied by both experimental and numerical methods. Using optical tweezers, the relationship of external force and relative extension is obtained by stretching single B-DNA molecule at 37°C. As the concentration increases from 0.909mM to 909mM, the overstretching transition force increases from 65.65 ± 1.2pN to 43.07 ± 1.2pN. An analytical expression is derived, which shows that overstretching transition force is linear with the natural logarithm of salt concentration. Based on a previous model, a three-dimensional model is proposed herein and solved by Metropolis Monte Carlo method. The bending deformation of DNA backbones, cooperativity of base-stacking interactions, electrostatic interactions, and spatial effects of DNA double helix structure are taken into account. Our key contribution is that the electrostatic energy is explicitly given as a function of folding angle and Na+ concentration. A new parameter is also introduced to account for the cooperativity of base-stacking interactions. The numerical results of this model are in good agreement with our experimental results.

The electrostatic contribution to DNA base-stacking interactions

Biopolymers ◽  
1992 ◽  
Vol 32 (2) ◽  
pp. 145-159 ◽  
Author(s):  
Richard A. Friedman ◽  
Barry Honig
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Dna Base ◽  
Electrostatic Contribution
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