New approach to DNA data storage makes system more dynamic, scalable


Date:
June 12, 2020
Source:
North Carolina State University
Summary:
Researchers have developed a fundamentally new approach to DNA
data storage systems, giving users the ability to read or modify
data files without destroying them and making the systems easier
to scale up for practical use.



FULL STORY ========================================================================== Researchers from North Carolina State University have developed a
fundamentally new approach to DNA data storage systems, giving users the ability to read or modify data files without destroying them and making
the systems easier to scale up for practical use.


========================================================================== "Most of the existing DNA data storage systems rely on polymerase
chain reaction (PCR) to access stored files, which is very efficient
at copying information but presents some significant challenges," says
Albert Keung, co- corresponding author of a paper on the work. "We've
developed a system called Dynamic Operations and Reusable Information
Storage, or DORIS, that doesn't rely on PCR. That has helped us address
some of the key obstacles facing practical implementation of DNA data
storage technologies." Keung is an assistant professor of chemical and biomolecular engineering at NC State.

DNA data storage systems have the potential to hold orders of magnitude
more information than existing systems of comparable size. However,
existing technologies have struggled to address a range of concerns
related to practical implementation.

Current systems rely on sequences of DNA called primer-binding sequences
that are added to the ends of DNA strands that store information. In
short, the primer-binding sequence of DNA serves as a file name. When you
want a given file, you retrieve the strands of DNA bearing that sequence.

Many of the practical barriers to DNA data storage technologies revolve
around the use of PCR to retrieve stored data. Systems that rely on
PCR have to drastically raise and lower the temperature of the stored
genetic material in order to rip the double-stranded DNA apart and
reveal the primer-binding sequence. This results in all of the DNA --
the primer-binding sequences and the data-storage sequences -- swimming
free in a kind of genetic soup. Existing technologies can then sort
through the soup to find, retrieve and copy the relevant DNA using
PCR. The temperature swings are problematic for developing practical technologies, and the PCR technique itself gradually consumes -- or uses
up -- the original version of the file that is being retrieved.

DORIS takes a different approach. Instead of using double-stranded
DNA as a primer-binding sequence, DORIS uses an "overhang" that
consists of a single- strand of DNA -- like a tail that streams behind
the double-stranded DNA that actually stores data. While traditional
techniques required temperature fluctuations to rip open the DNA in order
to find the relevant primer-binding sequences, using a single-stranded
overhang means that DORIS can find the appropriate primer-binding
sequences without disturbing the double-stranded DNA.

"In other words, DORIS can work at room temperature, making it much more feasible to develop DNA data management technologies that are viable in
real- world scenarios," says James Tuck, co-corresponding author of the
paper and a professor of electrical and computer engineering at NC State.

The other benefit of not having to rip apart the DNA strands is that the
DNA sequence in the overhang can be the same as a sequence found in the
double- stranded region of the data file itself. That's difficult to
achieve in PCR- based systems without sacrificing information density
-- because the system wouldn't be able to differentiate between
primer-binding sequences and data- storage sequences.

"DORIS allows us to significantly increase the information density of
the system, and also makes it easier to scale up to handle really large databases," says Kevin Lin, first author of the paper and a Ph.D. student
at NC State.

And once DORIS has identified the correct DNA sequence, it doesn't rely
on PCR to make copies. Instead, DORIS transcribes the DNA to RNA, which
is then reverse-transcribed back into DNA which the data-storage system
can read. In other words, DORIS doesn't have to consume the original
file in order to read it.

The single-stranded overhangs can also be modified, allowing users to
rename files, delete files or "lock" them -- effectively making them
invisible to other users.

"We've developed a functional prototype of DORIS, so we know it works,"
Keung says. "We're now interested in scaling it up, speeding it up and
putting it into a device that automates the process -- making it user friendly."

========================================================================== Story Source: Materials provided by North_Carolina_State_University. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Kevin N. Lin, Kevin Volkel, James M. Tuck, Albert J. Keung. Dynamic
and
scalable DNA-based information storage. Nature Communications,
2020; 11 (1) DOI: 10.1038/s41467-020-16797-2 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/06/200612111427.htm

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