Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Harp, Joel M.; Coates, Leighton; Sullivan, Brendan; Egli, Martin

doi:10.1093/nar/gkab264

Cited by 11 publications

(17 citation statements)

References 47 publications

(30 reference statements)

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“…S2). This feature had already been correctly predicted in the 1990s (Harper et al, 1998) and was confirmed by the current results, where the predicted hydration sites are in good agreement with the water positions solved by neutron diffraction (PDB entry 7jy2; Harp et al, 2021). Now, with hydration data for both the base and backbone, we observe a spherical water density HS forming a bridge between the N2(G) minor-groove atoms and the OP2 atom of the following phosphate.…”

Section: Tablesupporting

confidence: 89%

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Biedermannová

Černý

Malý

et al. 2022

Acta Crystallogr D Struct Biol

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Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.

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Section: Tablesupporting

confidence: 89%

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Biedermannová

Černý

Malý

et al. 2022

Acta Crystallogr D Struct Biol

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“…The Z II conformation has not been observed in any Z-RNA molecules of natural sequence [ 9 , 10 ]. The rotation of the GpC phosphate into a Z II conformation, as seen in Z-DNA structures [ 33 ], would bring the OP1 oxygen within ~2.3 Å of guanosine’s 2′OH, and may contribute to unfavorable repulsive forces.…”

Section: Structural Characteristics Of the Z-conformationmentioning

confidence: 99%

“…Theoretical work [ 67 , 68 ], ab initio modeling [ 62 , 63 ], and experimental studies [ 1 , 27 , 28 , 29 , 30 , 31 , 64 , 69 ] all suggest that the physical explanation for this increased stability is due to water-mediated hydrogen bonding networks facilitated by the exocyclic N2 group of guanosine residues, which is absent in adenosine residues. In the Z-conformation, N2 aminos of syn guanine bases form water-mediated hydrogen bond networks involving nearby phosphate groups ( Figure 5 A) [ 10 , 33 ]. Adenine, lacking an N2 amino group, is unable to make the same bridging connection and stabilize the syn conformation as effectively.…”

Section: Formation and Stability Of Z-conformationsmentioning

confidence: 99%

“…These water molecules were thought to form a “spine of hydration”, as has been well quoted in the literature. However, recent cryo neutron crystallography results suggest that these waters form a different network [ 33 ]. Water molecules are actually oriented such that they are unlikely to connect successive O2 groups ( Figure 7 ), instead forming a series of pentamers and hexamers that connect the interstrand phosphates across the minor groove [ 33 ].…”

Section: Formation and Stability Of Z-conformationsmentioning

confidence: 99%

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Structure and Formation of Z-DNA and Z-RNA

et al. 2023

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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 structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.

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“…However, most theoretical and computational studies are carried out in either a dilute environment or in the absence of water molecules. A recent study demonstrated how water molecules donate or accept hydrogen bonds within prominent parts of the DNA structure, including inside grooves and around the sugar–phosphate backbone [ 126 ]. This opens up new possibilities for studying how molecular crowders affect DNA structure and function with the presence of water around DNA.…”

Section: Dna In a Crowded Solutionmentioning

confidence: 99%

Structure and Dynamics of dsDNA in Cell-like Environments

Singh

Maity

Singh

2022

Entropy

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Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

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Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Cited by 11 publications

References 47 publications

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Structure and Formation of Z-DNA and Z-RNA

Structure and Dynamics of dsDNA in Cell-like Environments

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