Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics

Severins, Ivo; Joo, Chirlmin; Noort, John van

doi:10.1016/j.molcel.2022.04.024

Molecular Cell

2022

DOI: 10.1016/j.molcel.2022.04.024

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Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics

Ivo Severins

Chirlmin Joo

John van Noort

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Cited by 7 publications

(1 citation statement)

References 96 publications

(200 reference statements)

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“…Because of advances in high-throughput sequencing and its low cost, the method is extensively available in many aspects of life science research, especially for analyzing genome-wide events ( Metzker 2010 ). New high-throughput sequencing–based methodologies and approaches are being developed for gene expression analysis, epigenetic information profiling, chromatin structure analysis, noncoding RNA evaluation, high-throughput screening, mutation detection, and so on ( Kolmar et al 2022 ; Severins et al 2022 ).…”

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Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing

et al. 2023

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Tn5 transposon tagments double-stranded DNA and RNA/DNA hybrids to generate nucleic acids that are ready to be amplified for high-throughput sequencing. The nucleic acid substrates for the Tn5 transposon must be explored to increase the applications of Tn5. Here, we found that the Tn5 transposon can transpose oligos into the 5′ end of single-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA sequencing, starting with as little as 30 pg of total RNA. Moreover, compared with traditional dUTP-based strand-specific RNA sequencing, this method detects more genes, has a higher strand specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.

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Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing

et al. 2023

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On‐Chip Fluorescent Sensor for Chemical Vapor Detection

Wang

Kerman³

et al. 2023

Adv Materials Technologies

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Organic thin‐film fluorescent sensor is an efficient tool for detecting trace chemical vapor, such as illegal drugs, explosives, nerve agents, and other dangerous substances due to its high sensitivity and quick response. However, most of the current device structures rely on space optics, which makes it challenging to integrate with complementary metal oxide semiconductor (CMOS) technology, and hence difficult for achieving chip‐level implementation. On the other hand, silicon nitride waveguide‐based photonics have recently shown strong potential for developing commercial‐scale fully integrated on‐chip gas sensors. In this work, to the best of the knowledge, the first chemical vapor detector based on fluorescence sensing is reported by the evanescent field of the waveguide on integrated photonic platform. By the simultaneous excitation and collection with the same waveguide, a detection limit of 0.19 and 93.7 ppb for methamphetamine and aniline, respectively, is achieved. Thanks to the good compatibility with CMOS fabrication processes, this on‐chip optical sensor can achieve production scalability as well as ease of integration with wearable electronic devices to meet the demands of portable, rapid detection. The technical route presented in this work provides a promising solution for compact, low‐cost fluorescence‐based gas sensors.

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Tn5 transposase: a key tool to decrypt random transposition

Xu,

Zhou,

Song

et al. 2024

Biotechnol Bioproc E

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Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics

Cited by 7 publications

References 96 publications

Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing

Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing

On‐Chip Fluorescent Sensor for Chemical Vapor Detection

Tn5 transposase: a key tool to decrypt random transposition

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