Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization DOI Creative Commons

Xueqi Zhao,

Yue Zhao,

Li Zhu

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(15)

Опубликована: Апрель 10, 2025

Cellular structure maintenance and function regulation critically depend on the composition spatial distribution of numerous membrane proteins. However, current methods face limitations in coverage data scalability, hindering comprehensive analysis protein interactions complex cellular nanoenvironment. Herein, we introduce p roximity- a ctivated D NA s canning e ncoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic are anchored at single end, enabling free swings within nanoscale range to perform global scanning, recording, accumulating information diverse proximal proteins random directions along unrestricted paths. PADSE-seq leverages autonomous cyclic cleavage single-stranded sequentially activate encoded distributed throughout local area. This process triggers strand displacement amplification bidirectional extension reactions, linking barcodes molecular tandem further generating millions billions amplicons embedded combinatorial identifiers for next-generation analysis. As proof concept, validated mapping over dozen kinds proteins, including HER1, EpCAM, PDL1, proximity HER2 breast cancer cell lines, demonstrating its ability decode multiplexed proximities nanoscale. Notably, observed around low-abundance target exhibited greater diversity across regions variable ranges. method offers massive access high-resolution interactions, paving way deeper insights into biological processes advancing field precision medicine.

Язык: Английский

Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization DOI Creative Commons

Xueqi Zhao,

Yue Zhao,

Li Zhu

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(15)

Опубликована: Апрель 10, 2025

Cellular structure maintenance and function regulation critically depend on the composition spatial distribution of numerous membrane proteins. However, current methods face limitations in coverage data scalability, hindering comprehensive analysis protein interactions complex cellular nanoenvironment. Herein, we introduce p roximity- a ctivated D NA s canning e ncoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic are anchored at single end, enabling free swings within nanoscale range to perform global scanning, recording, accumulating information diverse proximal proteins random directions along unrestricted paths. PADSE-seq leverages autonomous cyclic cleavage single-stranded sequentially activate encoded distributed throughout local area. This process triggers strand displacement amplification bidirectional extension reactions, linking barcodes molecular tandem further generating millions billions amplicons embedded combinatorial identifiers for next-generation analysis. As proof concept, validated mapping over dozen kinds proteins, including HER1, EpCAM, PDL1, proximity HER2 breast cancer cell lines, demonstrating its ability decode multiplexed proximities nanoscale. Notably, observed around low-abundance target exhibited greater diversity across regions variable ranges. method offers massive access high-resolution interactions, paving way deeper insights into biological processes advancing field precision medicine.

Язык: Английский

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