Special Chemical Biology Seminar (via Video Conference)

DNA base pairs can form a transient structure, Hoogsteen base-pairing, alternating with canonical Watson-Crick-Franklin base-pairing, and present the DNA double helix with unique chemical and biological characteristics. We characterized this transient structure in double-stranded DNA and RNA using solution-state NMR relaxation dispersion technique and found that the formation of Hoogsteen base-pairing features a fundamental difference between DNA and RNA double helices. While Hoogsteen base pairs occur widely in B-form DNA double helices, they are absent in A-form RNA. Consequently, chemical modifications such as 1-methyladenosine and 1-methylguanosine, which can be accommodated as Hoogsteen base pairs in DNA duplexes, cause severe melting or secondary structure switching in double-stranded RNA. The presence of Hoogsteen base pairs in B-form DNA and its absence in A-form RNA can play important roles in DNA damage repair, genome integrity, and RNA functions.

Chemical modifications in RNA are highly relevant in biological processes such as differentiation, development, and diseases. Recent applications of next-generation sequencing technology in detecting chemical modifications enabled the identification of different types of chemical modifications across the transcriptome. However, resolution, sensitivity, and reproducibility remain major challenges for confident determinations of chemical modifications. We recently developed and validated a directed evolution platform to generate a robust and efficient reverse transcriptase that encodes chemical modifications as mutational signatures, demonstrated by engineering a reverse transcriptase for 1-methyladenosine. This evolved reverse transcriptase enabled us to map hundreds of 1-methyladenosine sites in human messenger RNA, many of which had previously eluded detection with existing methods. Our highly adaptable platform can be customized to detect other types of modifications, facilitating epitranscriptomic research.