Molecular Structure and Dynamics of DNA/RNA Helices

A special issue of DNA (ISSN 2673-8856).

Deadline for manuscript submissions: 15 July 2026 | Viewed by 1322

Special Issue Editor

Special Issue Information

Dear Colleagues,

Nucleic acids are the most important macromolecules for the continuity of life, among which DNA and RNA chains are well known. Knowledge concerning the molecular structure of these DNA/RNA helices, simplified michrohelices, or WC pairs of nucleosides or nucleobases is of great importance. Therefore, unpublished theoretical or experimental manuscripts that report on any aspect of the physical, chemical, and biochemical aspectrs of nucleic acids bases, nucleosides, nucleotides, DNA and RNA helices, and the interactions involved with them are welcome for this Special Issue. In addition, computationsl studies that deal with structure prediction, DFT calculations, molecular dynamics, or spectroscopy are accepted.Topics in this Special Issue may also include the following:

  • Effects of the different nucleosides in a strand on the helical parameters of the helix;
  • Influence of the different chemotherapeutic drugs on the DNA/RNA helix structure;
  • Effect of the mutations on the DNA/RNA replication and its mechanism. 

Dr. Mauricio Alcolea Palafox
Guest Editor

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Keywords

  • DNA/RNA structure
  • structure predictions
  • molecular simulations
  • molecular dynamics
  • microhelices
  • nucleosides structure
  • biomolecular interactions
  • DFT calculationsdeter
  • spectroscopic predictions
  • X-ray determination
  • drug effects on DNA/RNA

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Published Papers (1 paper)

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Research

16 pages, 810 KB  
Article
Computational Prediction of DNA-RNA Triplex Formation Sites Reveals Novel Regulatory Links Between lncRNAs and Key Fertility Genes in Retinta Cattle
by María Ángeles Vargas-Pérez, Chiraz Ziadi, Rosa María Morales, Sebastián Demyda-Peyrás, Gabriel Anaya Calvo-Rubio and Antonio Molina
DNA 2026, 6(2), 24; https://doi.org/10.3390/dna6020024 - 12 May 2026
Viewed by 366
Abstract
Background: Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression, playing pivotal roles in diverse biological processes, including reproduction. This study identified and characterized lncRNAs located near fertility-associated genes in Retinta beef cattle, exploring their potential regulatory roles via [...] Read more.
Background: Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression, playing pivotal roles in diverse biological processes, including reproduction. This study identified and characterized lncRNAs located near fertility-associated genes in Retinta beef cattle, exploring their potential regulatory roles via DNA–RNA triplex formation using in silico approaches. Methods: We applied an integrative bioinformatics pipeline to identify potential triplex interactions, predicting structurally accessible regions within the lncRNAs and demonstrating the statistical enrichment of binding sites across known regulatory genomic elements. Results: Twelve protein-coding genes previously linked to female fertility or male scrotal circumference were analyzed, revealing 16 unique lncRNAs within ±50 kb windows, predominantly on BTA5. We predicted high-confidence triplex-forming oligonucleotides (TFOs) for most gene-lncRNA pairs. Our results suggest robustness and sequence specificity, as interactions were disrupted by sequence permutation or when a control background sequence was used. RNA secondary-structure analysis revealed that TFOs generally lie in exposed regions, supporting their accessibility for triplex formation. Furthermore, promoter and regulatory regions of fertility-associated genes were enriched in predicted triplex target sites (TTSs), with some overlapping CpG islands and enhancer regions, leading to the hypothesis that these lncRNAs might play a role in epigenetic regulation. Conclusions: Overall, these findings establish computationally derived hypotheses regarding the potential molecular mechanisms by which lncRNAs may modulate reproductive efficiency in cattle and highlight specific lncRNAs as promising targets for functional studies and marker-assisted breeding. Full article
(This article belongs to the Special Issue Molecular Structure and Dynamics of DNA/RNA Helices)
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