Cell-surface glycoRNAs participate in diverse biological processes, but they were investigated as pooled populations and the protein interactome of individual glycoRNA species remain unresolved. Here we develop GlycoRNA-Map, a programmable photocatalytic proximity-labeling method that maps proteins surrounding sequence-defined endogenous glycoRNAs on living cells. A sialic-acid-binding aptamer and an RNA-hybridization probe jointly recruit a fluorophore-modified oligonucleotide through dual recognition of the glycan and RNA moieties of glycoRNAs. Light-activated biotinylation followed by quantitative mass spectrometry identified 200-418 enriched proteins for each of five glycoRNAs in A549 cells. Comparison of these proteomes revealed limited overlap among different glycoRNA sequences and across cell types, demonstrating that glycoRNA-associated protein environments depend on both RNA identity and cellular context. Transforming growth factor-{beta} receptors 1 and 2 (TGFBR1 and TGFBR2) were identified in the proximal proteomes of multiple glycoRNAs. Removal of cell-surface RNAs enhanced TGF-{beta} receptor signaling and promoted cell migration, demonstrating that glycoRNAs can functionally regulate extracellular signaling by interacting with their protein neighborhoods. GlycoRNA-Map thus provides an accessible strategy for resolving sequence-specific glycoRNA-protein interactome and discovering their roles in membrane signaling.

Chemical modifications of aptamers can enhance binding properties, however, the design of suitable functional groups remains challenging. Here, the authors introduce cyclooctatetraene (COT)-modified nucleotides in SELEX experiments, identifying COT-aptamers with low nM dissociation constants, highlighting the potential of three-dimensional ligands in aptamer discovery.

Recent advancement in molecular medicine has seen applications of advanced biotechnology tools such as aptamer technology in therapeutics and diagnostics. Aptamer technology has witnessed various approaches including "Click-Chemistry" towards modifying aptamer structure to improve its potentials, bu

**Abstract:** This research introduces a novel methodology for improving the fidelity and amplification efficiency of DNA polymerase switching events within modified aptamer structures. Utilizing hyper-dimensional stochastic optimization (HDSO) coupled with precise aptamer architecture engineering, we demonstrate a significant reduction in polymerase error incorporation rates and an increased overall amplification yield compared to conventional approaches. This method exhibits immediate commercial potential in point-of-care diagnostics, CRISPR-based gene editing and synthetic biology applications, with near-term scalability demonstrating viability for routine manufacturing.

Aptamer-based biosensors offer several advantages for detecting small molecules, including chemical stability and compatibility with diverse sensing formats. However, developing highly specific DNA ap...

SFM4-3, KOD DGLNK, and Therminator polymerase are investigated for their compatibility with SELection with Modified Aptamers (SELMA), an aptamer discovery method that enables incorporation of large nu...

Communications Chemistry, Published online: 15 September 2025; doi:10.1038/s42004-025-01629-5Chemical modifications of aptamers can enhance binding properties, however, the design of suitable functional groups remains challenging. Here, the authors introduce cyclooctatetraene (COT)-modified nucleotides in SELEX experiments, identifying COT-aptamers with low nM dissociation constants, highlighting the potential of three-dimensional ligands in aptamer discovery.

Decoration of aptamers with chemical modifications at the level of nucleobases grants access to alternative binding modes which often result in improved binding properties. Most functional groups invo...

The discovery of aptamers generally relies on laborious multiple-round selections with low success rate. Here, authors report the rapid, single-round selection of highly specific base-modified aptamer...

Discovery of functional nucleic acids from randomized libraries typically relies on multiple, time-consuming iterative rounds of in vitro selection with low success rate. Here, we present a single-round selection strategy for rapid screening of multiple over-represented nucleobase-modified DNA libraries and various selection conditions, capable of identifying high-affinity modified aptamers. Double partition followed by amplification of eluted sequences, NGS analysis and clustering provides fast identification of aptamer candidates. Screening of modified DNA libraries containing modified adenine and uracil nucleotides bearing hydrophobic aromatic phenyl and indole moieties results in development of an aptamer binding human insulin receptor with sub-nanomolar affinity and exquisite specificity. Cryo-EM structure reveals the importance of each aromatic modification, either in stabilizing the secondary structure or facilitating interactions with the protein surface. This approach addresse

A phosphorothioate-modified aptamer PT f -SRiApt capable of disrupting “undruggable” transcription factor SCAF4-POLR2A interaction with high inhibitory activity and biological stability is presented here. Through this inhibition, PT f -SRiApt successfully arrested cell cycle progression, induced cell death, and elevated immune recruitment in SCAF4-POLR2A-high triple-negative breast cancer. This novel inhibitor also demonstrated potential clinical efficacy in combination with immune checkpoint blockade in a wide range of cancers. Abstract The interaction between SCAF4 and RNA polymerase II (POLR2A) is crucial for proper mRNA termination, with its dysregulation leading to truncated mRNAs and nonfunctional proteins, impairing cellular growth. Despite its potential relevance, the role of this interaction in triple-negative breast cancer (TNBC) remains unexplored due to the lack of effective molecular tools. To address this, we employed SRiApt, an aptamer generated through the recently established Blocker-SELEX pipeline. Its biological stability is improved by phosphorothioate modifications to form PT f -SRiApt. Using this aptamer, the critical role of the SCAF4-POLR2A interaction in driving TNBC tumor growth and immune regulation is uncovered. PT f -SRiApt effectively inhibits tumor growth and induces cell cycle arrest in TNBC cells with elevated SCAF4 and POLR2A expression. Additionally, PT f -SRiApt promotes premature mRNA termination, boosting antigen presentation and promoting T-cell infiltration. Analysis of patient samples further confirmed the negative correlation between SCAF4-POLR2A interaction and the effectiveness of immunotherapy, highlighting the potential of PT f -SRiApt in improving immune efficacy. Together, the work provides a powerful tool not only for dissecting previously “undruggable” protein-protein interactions but also for enhancing tumor immunogenicity and reshaping the tumor microenvironment.