Comparison of Cis- and Oxaliplatin-induced Destabilization of 15-mer DNA- and RNA Duplexes by Binding to Centrally Located GG- and GNG Sequences

2013 ◽  
Vol 639 (8-9) ◽  
pp. 1655-1660 ◽  
Author(s):  
Christopher Polonyi ◽  
Ingrid Albertsson ◽  
Mariana S. Damian ◽  
Sofi K. C. Elmroth
Keyword(s):  
Dna And Rna ◽  
Rna Duplexes

scholarly journals The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

2021 ◽  
Vol 7 (17) ◽  
pp. eabf6106
Author(s):  
Weiwei He ◽  
Yen-Lin Chen ◽  
Lois Pollack ◽  
Serdal Kirmizialtin
Keyword(s):  
Structural Diversity ◽  
Conformational Ensemble ◽  
Structural Variations ◽  
Dna And Rna ◽  
X Ray Scattering ◽  
Double Stranded Dna ◽  
Binding Partners ◽  
Rna Duplexes ◽  
Dynamics Simulations ◽  
Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

Thermodynamics of nucleic acids and their interactions with ligands

2000 ◽  
Vol 33 (3) ◽  
pp. 255-306 ◽  
Author(s):  
Andrew N. Lane ◽  
Terence C. Jenkins
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Large Scale ◽  
Wide Spectrum ◽  
Model Systems ◽  
Linear Polymers ◽  
Dna And Rna ◽  
Rna Duplexes ◽  
Scale Properties ◽  
Folded Structures

1. Introduction 2551.1 General thermodynamics 2562. Nucleic acid thermodynamics 2602.1 DNA duplexes 2612.2 RNA duplexes 2632.3 Hybrid DNA–RNA duplexes 2642.4 Hydration 2672.5 Conformational flexibility 2692.6 Thermodynamics 2723. Nucleic acid–ligand interactions 2773.1 Minor groove binders 2783.2 DNA intercalators 2843.3 Triple-helical systems 2883.3.1 Structures 2883.3.2 Hydration 2913.3.3 Thermodynamics 2914. Conclusions 2955. Acknowledgements 2986. References 298In recent years the availability of large quantities of pure synthetic DNA and RNA has revolutionised the study of nucleic acids, such that it is now possible to study their conformations, dynamics and large-scale properties, and their interactions with small ligands, proteins and other nucleic acids in unprecedented detail. This has led to the (re)discovery of higher order structures such as triple helices and quartets, and also the catalytic activity of RNA contingent on three-dimensional folding, and the extraordinary specificity possible with DNA and RNA aptamers.Nucleic acids are quite different from proteins, even though they are both linear polymers formed from a small number of monomeric units. The major difference reflects the nature of the linkage between the monomers. The 5′–3′ phosphodiester linkage in nucleic acids carries a permanent negative charge, and affords a relatively large number of degrees of freedom, whereas the essentially rigid planar peptide linkage in proteins is neutral and provides only two degrees of torsional freedom per backbone residue. These two properties conspire to make nucleic acids relatively flexible and less likely to form extensive folded structures. Even when true 3D folded structures are formed from nucleic acids, the topology remains simple, with the anionic phosphates forming the surface of the molecule. Nevertheless, nucleic acids do occur in a variety of structures that includes single strands and high-order duplex, triplex or tetraplex (‘quadruplex’) forms. The principles of biological recognition and the related problem of understanding the forces that stabilise such folded structures are in some respects more straightforward than for proteins, making them attractive model systems for understanding general biophysical problems. This view is aided by the relatively facile chemical synthesis of pure nucleic acids of any desired size and defined sequence, and the ease of incorporation of a wide spectrum of chemically modified bases, sugars and backbone linkers. Such modifications are considerably more difficult to achieve with oligopeptides or proteins.

Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes

2014 ◽  
Vol 12 (37) ◽  
pp. 7366-7374 ◽  
Author(s):  
Sandip A. Shelke ◽  
Gunnar B. Sandholt ◽  
Snorri Th. Sigurdsson
Keyword(s):  
Spin Labeling ◽  
Spin Labels ◽  
Abasic Site ◽  
Abasic Sites ◽  
Dna And Rna ◽  
Rna Duplexes ◽  
Nitroxide Spin Labels ◽  
Uracil Derivative

Of ten new pyrimidine-derived nitroxide spin labels, an N1-ethylamino triazole-linked uracil derivative binds fully to both DNA and RNA duplexes containing an abasic site, as determined by CW-EPR.

scholarly journals Symmetry in Nucleic-Acid Double Helices

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 737
Author(s):  
Udo Heinemann ◽  
Yvette Roske
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Rna Structure ◽  
Test Tube ◽  
Base Pairs ◽  
Dna And Rna ◽  
Left Handed ◽  
Double Helices ◽  
Rna Duplexes ◽  
The Right

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

scholarly journals NMR study on the interaction of the conserved CREX ‘stem–loop’ in the Hepatitis E virus genome with a naphthyridine-based ligand

2015 ◽  
Vol 13 (37) ◽  
pp. 9665-9672 ◽  
Author(s):  
N. Dyubankova ◽  
M. Froeyen ◽  
M. Abramov ◽  
H. P. Mattelaer ◽  
P. Herdewijn ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Virus Genome ◽  
Stem Loop ◽  
Dna And Rna ◽  
Nmr Study ◽  
Rna Duplexes

A 2-amino-1,8-naphthyridine derivative that is described to bind single guanine bulges in RNA–DNA and RNA–RNA duplexes was synthesized and its interaction with the single G bulge in the conserved CREX of the Hepatitis E Virus (HEV) genome was explored by NMR and molecular modeling.

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