Song Lu

Rapid and accurate nucleic acid analysis is essential for disease diagnostics and drug development, yet persistent metal cation interference severely limits mass spectrometry’s effectiveness. We developed a liquid-phase ion trap (LPIT) system that utilizes strong electric fields to simultaneously dissociate metal contaminants and enrich purified nucleic acid ions directly in solution. This dual-action mechanism simplifies complex mass spectra, achieving up to a 48-fold improvement in mass accuracy and a 100-fold enhancement in signal intensity for intact DNA molecules. The platform’s versatility was demonstrated through high-resolution genetic variation analysis, rapid influenza virus subtyping from raw PCR products, and precise impurity detection in therapeutic drugs. By eliminating laborious pretreatment, the LPIT-ESI-MS system establishes a robust platform for high-fidelity genotyping and the rigorous analysis of therapeutic oligonucleotides, accelerating both clinical diagnostics and biopharmaceutical quality control.

The sequencing of synthetic oligonucleotides is fundamental to life sciences and therapeutics, yet current analytical approaches present inherent technical drawbacks of varying degrees. Hybridization‐based techniques cannot sequence the oligonucleotide primers they rely on, while the accuracy of mass spectrometry (MS)‐based techniques significantly diminishes as fragment length increases. Here, we introduce a liquid‐phase ion trap (LPIT) coupled with electrospray ionization (ESI)‐MS as a solution for rapid, high‐fidelity oligonucleotide sequencing. The LPIT utilizes a strong electric field to efficiently dissociate confounding metal cation adducts prior to MS analysis, resulting in cleaner spectra and enhanced signal intensity. This “desalting‐first” approach enables direct, rapid oligonucleotide analysis, achieving mass measurement accuracy comparable to benchmark liquid chromatography‐ESI‐MS (LC‐ESI‐MS) platforms. By integrating this platform with an exonuclease digestion workflow, we achieved full sequence coverage of oligonucleotides in under 30 min, a dramatic improvement in speed over existing methods. This work establishes LPIT‐ESI‐MS as a powerful platform for the direct and rapid sequencing of long oligonucleotides, addressing a critical unmet need in biotechnology and drug development.

Genomic structural variants (SVs) play a pivotal role in driving the evolution of hematologic malignancies, particularly in leukemia, in which genetic abnormalities are crucial features. Detecting SVs is essential for achieving precise diagnosis and prognosis in these cases. Karyotyping, often complemented by fluorescence in situ hybridization and/or chromosomal microarray analysis, provides standard diagnostic outcomes for various types of SVs in front‐line testing for leukemia. Recently, optical genome mapping (OGM) has emerged as a promising technique due to its ability to detect all SVs identified by other cytogenetic methods within one single assay. Furthermore, OGM has revealed additional clinically significant SVs in various clinical laboratories, underscoring its considerable potential for enhancing front‐line testing in cases of leukemia. This review aims to elucidate the principles of conventional cytogenetic techniques and OGM, with a focus on the technical performance of OGM and its applications in diagnosing and prognosticating myelodysplastic syndromes, acute myeloid leukemia, acute lymphoblastic leukemia, and chronic lymphocytic leukemia.

Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.