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Nucleic Acid Memory - Boise State University

Position: Research Scientist (2019-2022)
Location: Material Science & Engineering Department, Boise State University
PI: Dr. Will Hughes

Project Overview

Development of a DNA-origami based digital storage platform for encoding, storing, and reading digital information using chemically synthesized DNA and super-resolution microscopy.

Concept

DNA offers information density and stability advantages over traditional storage media:

  • Information density: DNA can store data at densities far exceeding hard drives
  • Stability: DNA remains stable for thousands of years under proper conditions
  • Energy efficiency: No power required for storage
  • Quaternary code: Uses A, G, C, T bases (4-state vs binary 2-state)

Technical Approach

DNA Origami Scaffold

  • Used bacteriophage DNA as scaffold
  • Programmed DNA to fold into "breadboard" structures
  • Positioned staple strands at specific locations to encode information

Data Encoding

  • Digital information encoded into DNA sequences
  • Staple strands positioned to represent binary data
  • Error-correction algorithms implemented

DNA-PAINT Readout

  • Super-resolution microscopy technique
  • Optically read encoded information at nanoscale resolution
  • Achieved successful data recovery from DNA

Key Achievement

Successfully encoded and optically read the message: "Data is in our DNA!"

This demonstrated proof-of-concept for DNA-based information storage with optical readout.

Techniques

Molecular Biology

  • DNA origami assembly
  • Oligonucleotide design and synthesis
  • DNA-PAINT probe development
  • Automated liquid handling (EpMotion system)

Microscopy

  • DNA-PAINT super-resolution imaging
  • Custom microscopy protocols
  • Image acquisition optimization

Computational

  • Error-correction algorithm development
  • Image analysis software
  • Data encoding/decoding pipelines

Publications

  1. Dickinson, GD, Mortuza G, Clay W, Piantanida L, Green C.M, Watson C, Hayden EJ, Andersen T, Kuang W, Graugnard E, Zadegan R, Hughes WL. (2021) An alternative approach to nucleic acid memory. Nature Communications 12:2371. PMID: 33888693

  2. Mortuza GM, Guerrero J, Llewellyn S, Tobiason MD, Dickinson GD, Hughes WL, Zadegan R, Andersen T. (2023) In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA). BMC Bioinformatics 24(1):160. PMID: 37085766

  3. Piantanida L, Dickinson GD, Majikes JM, Clay W, Liddle JA, Andersen T, Hayden EJ, Kuang W, Hughes WL. (2024) DNA-PAINT Probe Modifications Support High-Resolution Imaging with Shorter Binding Domains. ACS Nano 18(33):22369-22377. PMID: 39109416

View all publications →

Patent

Nucleic acid memory (NAM) / digital nucleic acid memory (DNAM)
US Patent App. 17/443,312 (2022)

Collaborative Team

Interdisciplinary collaboration across multiple departments: - Materials Science & Engineering - Computer Science - Biological Sciences - Electrical & Computer Engineering

This research built upon earlier DNA-PAINT work by Ralf Jungmann (Ludwig Maximilian University of Munich) and represents a novel approach to nucleic acid-based information storage.

Page last updated: December 2024