eSENSE Break provides the nucleotide-level fragmentation data you need to diagnose integrity issues, refine sequence and process decisions, and support regulatory characterization.
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Diagnose IVT RNA integrity issues at their source
Standard integrity assays measure IVT RNA quality at low resolution but cannot identify where fragmentation is occurring or what is driving it. eSENSE Break, part of our eMERGE characterization platform, uses next-generation sequencing to map fragmentation sites across linear or circular RNA therapeutics at single-nucleotide resolution. The result is positional data you can act on: pinpoint hotspots, compare conditions, and make confident decisions about sequence design and manufacturing.
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Use:
Map fragmentation sites, map circular RNA nicking sites, diagnose integrity issues
Typical samples:
IVT mRNA, saRNA/srRNA, circRNA
How eSENSE Break works
Pinpoint every break across your sequence
Contact usPrepare libraries
Sequencing libraries are generated from IVT RNAs
Sequence
Next-generation sequencing is performed
Analyze
Custom bioinformatics analyses determine breakage sites
Nucleotide-level insights
eSENSE Break is exclusive to our eMERGE and eCOMPASS platforms. Each engagement is scoped to your program.
Pinpoint fragmentation hotspots
Standard integrity assays report integrity at low resolution; they cannot tell you which nucleotide positions are breaking. eSENSE Break uses next-generation sequencing to generate a positional map of fragmentation sites across your IVT RNA therapeutic, showing exactly where breaks are occurring. Knowing where breaks occur tells you what to change: the sequence, the process, or both.
A fragment spiked into an intact RNA results in a single positional peak, with no false signal across the rest of the 1.8 kb sequence.
Determine why fragmentation occurs
Without positional data, diagnosing the source of RNA degradation requires extensive experimental guesswork. If fragmentation localizes at specific sequence motifs, the cause is sequence-driven; paired with eSHAPE structural profiling, the data reveals how RNA secondary structure relates to fragmentation patterns. If the pattern shifts across IVT conditions, formulation variables, or storage timepoints, the cause is process-driven. Either way, the data points you to the source.
Top: RNA secondary structure mapped with eSHAPE, our proprietary structural profiling assay. Bottom: eSENSE Break detections. Breaks localize to unpaired bases in this mRNA, pointing to a sequence-driven cause.