[HTML][HTML] Structure and formation of Z-DNA and Z-RNA

JB Krall, PJ Nichols, MA Henen, Q Vicens, B Vögeli - Molecules, 2023 - mdpi.com
Despite structural differences between the right-handed conformations of A-RNA and B-
DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their …

Z-RNA biology: a central role in the innate immune response?

PJ Nichols, JB Krall, MA Henen, B Vögeli, Q Vicens - RNA, 2023 - rnajournal.cshlp.org
Z-RNA is a higher-energy, left-handed conformation of RNA, whose function has remained
elusive. A growing body of work alludes to regulatory roles for Z-RNA in the immune …

Mg2+ ions: do they bind to nucleobase nitrogens?

F Leonarski, L d'Ascenzo, P Auffinger - Nucleic acids research, 2017 - academic.oup.com
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately
determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere …

Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate

PJ Nichols, JB Krall, MA Henen, R Welty… - Journal of the …, 2023 - ACS Publications
The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA
when bound by Zα domains found within a variety of innate immune response proteins. Zα …

[HTML][HTML] Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

N Foloppe, B Hartmann, L Nilsson, AD MacKerell - Biophysical Journal, 2002 - cell.com
The glycosyl torsion (χ) in nucleic acids has long been recognized to be a major determinant
of their conformational properties. χ torsional energetics were systematically mapped in …

A single watson− crick G· C base pair in water: aqueous hydrogen bonds in hydrophobic cavities

T Sawada, M Fujita - Journal of the American Chemical Society, 2010 - ACS Publications
Hydrogen bond (H-bond) formation in water has been a challenging task because water
molecules are constant competitors. In biological systems, however, stable H-bonds are …

Hydration of short DNA, RNA and 2′‐OMe oligonucleotides determined by osmotic stressing

E Rozners, J Moulder - Nucleic acids research, 2004 - academic.oup.com
Studies on hydration are important for better understanding of structure and function of
nucleic acids. We compared the hydration of self‐complementary DNA, RNA and 2′‐O …

[HTML][HTML] Searching for new Z-DNA/Z-RNA binding proteins based on structural similarity to experimentally validated Zα domain

M Bartas, K Slychko, V Brázda, J Červeň… - International Journal of …, 2022 - mdpi.com
Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which
play a significant role in several molecular and biological processes including DNA …

'Z-DNA like'fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response

L d'Ascenzo, F Leonarski, Q Vicens… - Nucleic acids …, 2016 - academic.oup.com
Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have
known that d (CpG) steps can adopt a particular structure that leads to forming left-handed …

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZα ADAR1

SC Ha, J Choi, HY Hwang, A Rich, YG Kim… - Nucleic acids …, 2009 - academic.oup.com
The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and
is specifically recognized by Zα domains identified in several Z-DNA-binding proteins. The …