RNA and DNA analysis using engineered surfaces

Provided herein are compositions and methods for multiplex profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of atypical features (e.g., base modifications, backbone modifications, impairments and/or structural elements) of a target nucleic acid with the step of writing information from the recognition event to a neighboring genetic sequence of the target nucleic acid using a barcode. And then converting the obtained nucleic acid coded by the bar code into a sequencing library, and reading through a DNA/RNA sequencing method. The steps reveal the sequence of the barcode that is associated with an atypical feature in the target nucleic acid. The high throughput profiling methods described herein allow for the recognition and/or localization of one or more modifications in a target nucleic acid. The methods also allow for the simultaneous recognition of the properties and locations of several or all DNA/RNA modifications. 本文提供了分别用于跨