CSBJ11h ago

🧬 If structure determines function, how can we optimize DNA therapeutics without accurately predicting their 3D shape?

🔗 Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0127

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #DNA #ComputationalBiology #Bioinformatics #MolecularBiology #Aptamers #DNANanotechnology #GenomeEngineering #NucleicAcids

Tom HowardMay 13

For anyone interested in, or working on, #NucleicAcids (in the broadest sense), we have just launched a new innovation network.

Details in the link, including how to sign up.

As this is a new network, with a broad remit, there is an opportunity to help shape its activities and priorities.

We also have some funds for training and network building activities coming along later.

The network is not exclusive to UK-participants and we welcome international colleagues.
https://www.ncl.ac.uk/press/articles/latest/2026/05/nucleicacidnetwork/

UK-wide nucleic acid network launches

Newcastle University is part of a new national network which will accelerate innovation across nucleic acids such as DNA and RNA.

Press Office
Benjamin Carr, Ph.D. 👨🏻‍💻🧬Apr 27
We keep finding the raw material of #DNA in #asteroids—what's it telling us?
There are four #nucleicacids (A, T, C, and G in DNA; A, U, C, and G in #RNA), and one is always attached to each of sugars in backbone. The order of the bases along the backbone is what carries genetic information, enabling life as we know it. It’s been hypothesized that, before life evolved, the order of bases along RNA molecules determined the sorts of chemical reactions they could catalyze.
https://arstechnica.com/science/2026/03/we-keep-finding-the-raw-material-of-dna-in-asteroids-whats-it-telling-us/
We keep finding the raw material of DNA in asteroids—what's it telling us?

This week's result is just the latest in a growing collection of discoveries.

Ars Technica
Piia BartosFeb 27

Our newest publication is out!

We showed that the yeast core factor (CF) binds and specifically recognizes promoter DNA in a two-step process, after which it will recruit RNA Polymerase I, inducing DNA bending and melting to start the transcription process.

https://academic.oup.com/nar/article/54/5/gkag153/8495788

#academicChatter #publication #science #nucleicAcidsResearch #nucleicAcids #yeast #dna #transcription

StructBiolCommunicationsFeb 19
This structure of a tRNA acceptor-stem mimic demonstrates the use of bromine and phosphorus anomalous scattering for RNA structure determination #Crystallography #AnomalousScattering #NucleicAcids https://doi.org/10.1107/S2053230X26000658
Stephan HackerDec 4, 2025
Very insightful review by the group of Alexander Deiters in @[email protected] They give an overview of the development of covalent #aptamers for protein labeling and inhibition including an overview of the chemistries used. doi.org/10.1039/d5cb... #ChemSky #ChemBio #NucleicAcids #RNA #DNA

Covalent aptamers: agents with...
Stephan HackerDec 4, 2025
Very insightful review by the group of Alexander Deiters in RSC Chemical Biology. They give an overview of the development of covalent #aptamers for protein labeling and inhibition including an overview of the chemistries used. https://doi.org/10.1039/d5cb00133a
#Chemistry #ChemBio #NucleicAcids #RNA #DNA
Show threadStephan HackerNov 25, 2025
She also talked about the formation of coacervates based on #DNA or #RNA as well as #peptides and their potential involvement in early life. (2/2) www.nature.com/articles/s41... #ChemSky #OriginOfLife #lipid #membrane #evolution #LipidTime #NucleicAcids

Differential stability and dyn...
Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry - Nature Communications

Mixtures of peptides and nucleic acids tend to demix and form coacervate droplets. Here, the authors show that even short peptides and oligonucleotides form droplets. DNA and RNA impart different properties to these protocells – stability, fluidity and the potential to host RNA chemistry.

Nature
Stephan HackerNov 25, 2025

How did primitive membranes form at the #OriginOfLife and how did they evolve into the cellular envelopes of modern cells?

Exciting talk by Claudia Bonfio about the non-enzymatic formation of phospholipids under conditions that are plausible for early Earth. https://pubs.rsc.org/en/content/articlelanding/2024/sc/d4sc05362a (1/2)

#Chemistry #OriginOfLife #lipid #membrane #evolution #LipidTime #NucleicAcids

Stephan HackerNov 24, 2025

Interesting bioRxiv preprint by the group of Matt Disney. They used fully functionalized fragments to enrich their targets and identify their binding sites on #RNA. Interesting insights into preferential binding to UTRs and the construction of RiboTACs.

https://www.biorxiv.org/content/10.1101/2025.11.05.686775v1
#NucleicAcids #TargetedDegradation #Chemistry #ChemBio

Live-Cell Covalent Profiling Reveals Principles of RNA-Small Molecule Recognition across the Human Transcriptome

RNA folds are abundant in mammalian cells yet poorly characterized as small-molecule targets. We present a scalable, unbiased live-cell pipeline that maps where small molecules bind RNA across the human transcriptome and convert those binders into selective degraders. A 200-member fragment library bearing diazirine/alkyne handles yielded 23 RNA-binding candidates. Chem-CLIP-Map-Seq in MDA-MB-231 cells identified 723 RNA targets and their binding sites, revealing a strong bias toward 5'; and 3'; untranslated regions (UTRs) in mRNAs and enrichment at thermodynamically stable structures, with limited binding to non-coding RNAs. Expression level and local stability contributed to engagement. An integrated machine-learning model trained on multiple fingerprints distinguished binders from non-binders, and highlighted chemotypes and physicochemical features that favor RNA recognition. Four fragments were converted to a Ribonuclease Targeting Chimera (RiboTAC) to recruit Rnase L to degrade targeted mRNAs. Despite broad binding, cleavage was highly selective, with X1-RiboTAC degrading MPP7 and SSC4D mRNAs in an RNase L-dependent manner and reducing their protein levels. A competitive profiling workflow quantified in-cell target occupancy and guided optimization of the RNA-binding module to reprogram selectivity: an X1 derivative produced an MPP7-selective RiboTAC that lowered MPP7 mRNA levels and suppressed breast-cancer cell migration, while sparing SSC4D transcripts. This end-to-end framework, including transcriptome-wide mapping, data-driven rules, and tunable degradation, establishes practical principles for ligandable RNA sites in cells and enables rational design of RNA-targeted small molecules and degraders. ### Competing Interest Statement MDD Is a founder of Expansion and Ribonaut therapeutics. JLC-D is a founder of Ribonaut therapeutics. NIH Common Fund, CA249180A NIH Common Fund, GM133810 NIH Common Fund, https://ror.org/001d55x84, CA257090 Muscular Dystrophy Association, https://ror.org/01frxsf98, 963835

bioRxiv