Parallel‐stranded DNA and RNA duplexes–structural features and potential applications

M Szabat, R Kierzek - The FEBS journal, 2017 - Wiley Online Library
Nowadays, decades after the discovery of the right‐handed B form of DNA, it is well known
that nucleic acids have great conformational flexibility, exhibiting a large degree of variation …

Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA

AK Jain, S Bhattacharya - Bioconjugate chemistry, 2010 - ACS Publications
DNA adopts different conformations not only based on novel base pairs, but also with
different chain polarities. Besides several duplex structures (A, B, Z, parallel stranded (ps) …

Intermolecular CH··· O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study

OO Brovarets', YP Yurenko… - Journal of Biomolecular …, 2014 - Taylor & Francis
This study aims to cast light on the physico-chemical nature and energetic of the non-
conventional CH··· O/N H-bonds in the biologically important natural nucleobase pairs using …

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

S Liu, P Peng, H Wang, L Shi, T Li - Nucleic Acids Research, 2017 - academic.oup.com
A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-
quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with …

NMR structure of a parallel-stranded DNA duplex at atomic resolution

VR Parvathy, SR Bhaumik, KVR Chary… - Nucleic acids …, 2002 - academic.oup.com
DNA dodecamers have been designed with two cytosines on each end and intervening A
and T stretches, such that the oligomers have fully complementary A: T base pairs when …

Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А· Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms

OO Brovarets', KS Tsiupa, DM Hovorun - Scientific Reports, 2018 - nature.com
In this study it was theoretically shown that discovered by us recently (Brovarets' et al.,
Frontiers in Chemistry, 2018, 6: 8; doi: 10.3389/fchem. 2018.00008) high-energetical …

Structure and Drug interaction of parellel-stranded DNA studies by infrared spectroscope and fluorence

H Fritzsche, A Akhebat, E Taillandier… - Nucleic acids …, 1993 - academic.oup.com
The infrared spectra of three different 25-mer parallelstranded DNAs (ps-DNA) have been
studied. We have used ps-DNAs containing either exclusively dA-dT base pairs or …

Local supercoil-stabilized DNA structure

E Paleček - Critical reviews in biochemistry and molecular biology, 1991 - Taylor & Francis
The DNA double helix exhibits local sequence-dependent polymorphism at the level of the
single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA …

Unexpected A· T (WC)↔ A· T (rWC)/A· T (rH) and A· T (H)↔ A· T (rH)/A· T (rWC) conformational transitions between the classical A· T DNA base pairs: A QM/QTAIM …

OO Brovarets', KS Tsiupa… - International Journal of …, 2018 - Wiley Online Library
In this study, using QM/QTAIM calculations in the continuum with ε= 1 under normal
conditions, we have revealed for the first time the nondissociative A· T (WC)↔ A· T (rWC)/A …

Surprising conformers of the biologically important A· T DNA base pairs: QM/QTAIM proofs

OO Brovarets', KS Tsiupa, DM Hovorun - Frontiers in Chemistry, 2018 - frontiersin.org
For the first time novel high-energy conformers–A· T (wWC)(5.36), A· T (wrWC)(5.97), A· T
(wH)(5.78), and A· T (wrH)(ΔG= 5.82 kcal· mol− 1)(See Graphical Abstract) were revealed for …