Urgent.News

What's breaking now, across thousands of outlets.

Monday, 10 August 2026 Reading Room

Science

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

The sequence-dependent mechanical landscapes of double-stranded nucleic acid (dsNA) remain largely unexplored beyond canonical dsDNA. We describe cgNA+, a coarse-grained predictive model of the mechanics of dsRNA, DNA:RNA hybrids, and epigenetically modified dsDNA, all parameterised from 1.26 milliseconds of atomistic simulations. cgNA+ predicts non-local sequence-dependent equilibrium shape and…

biorxiv.org ·

The study explores the sequence-dependent mechanical landscapes of double-stranded nucleic acids (dsNA), with a focus on double-stranded RNA (dsRNA), DNA-RNA hybrids, and epigenetically modified double-stranded DNA (dsDNA). A coarse-grained predictive model called cgNA+ was developed to simulate the mechanics of these dsNA types, using data from a mere 1.26 milliseconds of atomistic simulations.

The model accurately predicts the non-local sequence-dependent equilibrium shape and stiffness of these dsNA structures, with errors an order of magnitude smaller than those observed in previous sequence-variability studies.

The research highlights the strong influence of flanking sequence up to an octamer context on the equilibrium shape of dsNA. Flexible dimer-steps were found to be more context-sensitive. Modification of CpG sites was shown to alter the equilibrium shape of dsNA as significantly as single-nucleotide polymorphisms. The groove width analysis across dsNA decamers revealed strong sequence dependence, reflecting the differing characteristic helical geometries of dsDNA and dsRNA. However, DRHs exhibited mixed behavior depending on the pyrimidine content of the DNA strand.

Cancer-related transcription factor CTCF binding sites demonstrated a distinct groove width signature. The persistence-length spectra from over [~]9 million sequences indicated that dsRNA is stiffer than dsDNA. However, DRH showed intermediate stiffness that was modulated by the DNA strand's pyrimidine content. Interestingly, persistence length increased upon CpG modification, but decreased upon hypermodification.

In conclusion, the cgNA+ model allows for the first highly accurate, very large-scale, and comparative study of sequence-dependent mechanics across different dsNA classes. This study uncovers previously hidden regulatory layers in the mechanics of dsNA, providing new insights into their sequence-dependent behavior.

Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.

Read the original at biorxiv.org →

More in Science

The heatwave is not just a temporary discomfort; it can have long-lasting effects on our bodies. Research has shown that a single episode of extreme heat can accelerate the biological aging process by as much as six months. This phenomenon is closely linked to climate change, which is causing temperatures to rise at an alarming rate. As the planet continues to warm up, the impact of heatwaves on human health is becoming increasingly evident. Heatwaves are not just a matter of discomfort; they can have serious consequences for our well-being. Prolonged exposure to high temperatures can lead to a range of health problems, from heat exhaustion to more severe conditions such as heatstroke. The biological clock, also known as the circadian rhythm, plays a crucial role in regulating our bodily functions. It is controlled by an intricate system that responds to light and darkness, and is influenced by external factors such as temperature and humidity. When we are exposed to extreme heat, our biological clock can get disrupted, leading to a range of physiological changes. Studies have shown that prolonged exposure to heat can lead to increased inflammation, oxidative stress, and DNA damage. These changes can accelerate the aging process, making us look and feel older than we actually are. In fact, research has shown that a single episode of extreme heat can increase biological age by as much as six months. The implications of this research are significant, particularly in the context of climate change. As temperatures continue to rise, we can expect to see more frequent and severe heatwaves. This means that we need to take urgent action to mitigate the effects of climate change and protect ourselves from the impacts of extreme heat. The Korean government has launched a series of initiatives to address the challenges posed by climate change. The Ministry of Environment has introduced a heatwave warning system, which provides early warnings to vulnerable populations such as the elderly and young children. The government has also launched a public awareness campaign to educate people on the risks associated with heatwaves and the steps they can take to protect themselves. In addition to these efforts, researchers are working to develop new technologies and strategies to mitigate the effects of heatwaves. For example, some scientists are exploring the use of cool roofs and green spaces to reduce urban heat islands. Others are developing new materials and systems that can help to keep buildings cool during extreme heat. As the world grapples with the challenges posed by climate change, it is clear that we need to take a proactive approach to protecting ourselves from the impacts of extreme heat. By working together, we can reduce the risks associated with heatwaves and create a more sustainable future for all.

·hani.co.kr

More from Monday 10 August →