… Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities
between Argonaute-miRNA complexes and all sequences ≤12 nucleotides in length. This …

RNA-guided nucleases (RGNs) provide sequence-specific gene regulation through base-pairing
interactions between a small RNA guide and target RNA or DNA. RGN systems, which …

Circular RNAs (circRNAs) are a class of single-stranded RNAs with a contiguous structure
that have enhanced stability and a lack of end motifs necessary for interaction with various …

The past decades have witnessed tremendous developments in our understanding of RNA
biology. At the core of these advances have been studies aimed at discerning RNA structure …

… We used RNA bind-n-seq with purified AGO2–miRNA complexes to measure relative
affinities of> 1000 3ʹ-pairing architectures for each miRNA. In some cases, optimal 3ʹ pairing …

… asymmetric loops up to three in length (N = 1,328; Figure S1B). In addition, we included a
set of junction sequences characterized by X-ray crystallography (N = 359) to relate energetic …

The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids
that profoundly affects their interactions with proteins and ligands. Experimental methods …

Electrostatics are central to all aspects of nucleic acid behavior, including their folding,
condensation, and binding to other molecules, and the energetics of these processes are …

… where T is the temperature, R is the universal gas constant, and N bound and N unbound
are the number of simulated structures annotated as bound or unbound, respectively. We …

… Namita Bisaria, Daniel Herschlag; Probing the kinetic and thermodynamic consequences
of the tetraloop/tetraloop receptor monovalent ion-binding site in P4–P6 RNA by smFRET. …