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Related Concept Videos

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Related Experiment Video

Updated: May 31, 2025

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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DNA Origami Framework-Based Spatial Nanochip for Circular ssDNA Assembly and Data Storage.

Shengwen Wang1, Donglei Yang1, Jiankai Li2

  • 1Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.

Small (Weinheim an Der Bergstrasse, Germany)
|January 23, 2025
PubMed
Summary

A novel 3D DNA spatial chip (DSC) enables efficient assembly of long circular DNA for data storage. This DNA data storage method enhances stability and allows multiplexed retrieval of encoded information.

Keywords:
DNA data storageDNA spatial chipcircular single‐stranded DNAconfined assemblynanopore sequencing

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Area of Science:

  • Biotechnology
  • Nanotechnology
  • Data Storage

Background:

  • DNA origami enables precise nanoscale construction.
  • Circular single-stranded DNA (c-ssDNA) offers a stable format for DNA data storage.
  • Efficient assembly and retrieval of long DNA molecules for data storage remain challenging.

Purpose of the Study:

  • To introduce a 3D DNA spatial chip (DSC) for constructing customized c-ssDNA for data storage.
  • To demonstrate multiplexed assembly and retrieval of multiple data files within a single DSC.
  • To evaluate the stability and integrity of DNA data stored using the DSC method.

Main Methods:

  • Utilized an icosahedral DNA origami framework to create a 3D DNA spatial chip.
  • Employed addressable location sequences on the DSC for directed assembly of oligonucleotides into c-ssDNA.
  • Applied rolling circle amplification (RCA) and nanopore sequencing for data retrieval.
  • Functionalized DSCs with fluorescent labels and capture sequences for magnetic bead-based retrieval.

Main Results:

  • Successfully constructed c-ssDNAs encoding two poems (800 and 860 nucleotides) from up to 15 fragments.
  • Achieved simultaneous assembly and readout of both poems within a single DSC using orthogonal location sites.
  • Demonstrated complete data retrieval using RCA and nanopore sequencing.
  • Confirmed data integrity after storage under various conditions.
  • Enabled rapid identification and retrieval of specific datasets from a mixture via magnetic beads.

Conclusions:

  • The 3D DNA spatial chip provides an efficient platform for assembling long c-ssDNA for data storage.
  • This approach overcomes limitations in DNA data storage by reducing redundancy and enhancing stability.
  • The DSC facilitates multiplexed storage and retrieval, paving the way for advanced DNA data archiving.