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Nanoscale view of several interwoven fragments of ‘doodled’ DNA (orange and white strands) imaged on a near perfectly flat mica surface (shown in blue) using a custom high-speed atomic force microscope built at the University of Bristol.
Image Credit: Thomas Gorochowski
Scientific Frontline: Extended "At a Glance" Summary: DNA Polymerase "Doodling"
The Core Concept: DNA polymerases—the microscopic biological machines responsible for replicating DNA—possess an innate capability to synthesize entirely new, highly complex, and extensive DNA sequences from scratch without utilizing an existing template.
Key Distinction/Mechanism: Standard DNA replication relies on reading and mirroring an existing DNA strand. Conversely, "doodling" involves the autonomous generation of distinct genetic material ranging from simple two-base repeats to elaborate eight-base motifs. Furthermore, unlike contemporary chemical DNA synthesis, which is slow and limited to sequences of a few hundred bases, this template-free synthesis can generate fragments exceeding 85,000 bases in a single reaction. Crucially, the process can be "steered" by modulating environmental parameters, such as altering the temperature or restricting the available DNA building blocks.
Major Frameworks/Components:
- Nanopore Sequencing: Utilized to map the full-length structures of thousands of autonomously generated DNA molecules, revealing unprecedented sequence complexity.
- Environmental Modulation: The methodology of altering reaction conditions (e.g., temperature shifts, reagent limitation) to dictate the specific repeating patterns and motifs synthesized by the polymerases.
- AI-Powered Protein Design: Proposed as an integrative framework to optimize and harness these biological machines for advanced, guided synthesis.
Branch of Science: Engineering Biology, Molecular Biology, Synthetic Biology, and Biotechnology.
Future Application: This process holds the potential to revolutionize how long DNA sequences are written. By integrating these findings with AI-driven protein engineering, scientists aim to establish highly efficient, single-reaction methods for the guided synthesis of kilobase-scale synthetic DNA, circumventing the bottlenecks of traditional chemical synthesis.
Why It Matters: The ability to efficiently and accurately manufacture long DNA fragments is currently a significant limiting factor in genetic research and engineering. Harnessing a biological machine's innate ability to rapidly "write" long sequences on demand provides a highly scalable alternative, fundamentally accelerating biotechnological advancements and offering new insights into how novel genetic information emerges organically.
New research has discovered that the molecular machines responsible for copying our DNA have a surprising hidden talent – an ability to create entirely new and highly sophisticated DNA sequences from scratch.
The study, led by the University of Bristol and published in Nature Communications, analyses this curious ‘doodling’ activity, showing for the first time that it can be steered and controlled. The findings not only help shed further light on how genetic information emerges but could also present exciting new ways of writing long DNA sequences.
Every time a cell divides, it needs to copy its DNA. This job falls to proteins called DNA polymerases – tiny biological machines that read an existing DNA strand and build a matching copy, letter by letter, essentially acting as nature’s photocopiers. It has been known, since the 1960s, that some of these machines can also build new DNA without anything to copy from, in a process scientists nicknamed ‘doodling’. Until now, the sequences produced by doodling have been poorly characterized, and this study provides the most detailed assessment to date.
Co-lead author Simeon Castle, who conducted the research as part of his PhD in Engineering Biology at the University of Bristol School of Biological Sciences, said: “We used nanopore sequencing to read the full-length sequences of thousands of DNA molecules that polymerases had created entirely on their own. What we found was far more diverse and complex than anyone had appreciated – from simple two-base repeats to elaborate eight-base motifs, all varying depending on which polymerase was used and the reaction conditions.”
Current methods for writing DNA rely on slow chemical processes and struggle to produce sequences longer than a few hundred bases (a base being the single letters from which DNA is built). By contrast, doodling can generate much longer fragments in a single reaction, with some exceeding 85,000 bases.
Co-lead author Thea Irvine, a PhD student in Engineering Biology at the University’s School of Biological Sciences, added: “One of the most exciting findings was that we could steer what the polymerases produced. By changing the temperature or limiting which DNA building blocks were available, we could shift the composition of the sequences generated.
“When we provided only two of the four building blocks present in DNA, the polymerase produced long stretches of highly regular repeating patterns – some over a thousand bases in length.”
Senior author Thomas Gorochowski, Professor of Biological Engineering and a Royal Society University Research Fellow at the University of Bristol, added: “Doodling by DNA polymerases has been known about for decades, but has largely been treated as a curiosity. Our work shows it is a tunable process with implications for how new genetic material is created and a real potential for biotechnology.
“Combining our findings with advances in AI-powered protein design, we believe harnessing doodling for the guided synthesis of long DNA sequences could be closer than many think.”
Funding: The study was supported by Replay Holdings Inc., the Royal Society, the Alan Turing Institute, the Medical Research Council (MRC), the UKRI Engineering and Physical Sciences Research Council (EPSRC) and UKRI Biotechnology and Biological Sciences Research Council (BBSRC). The research united multidisciplinary experts from the University of Bristol, University of St. Andrews, and the Medical Research Council (MRC) Laboratory of Molecular Biology in the UK, and The Centre of Excellence for Engineering Biology in New York and Replay Holdings Inc. in the USA.
Published in journal: Nature Communications
Authors: Simeon. D. Castle, Thea C. T. Irvine, Adrian Woolfson, Gregory Linshiz, Blake T. Riley, Ifor D. W. Samuel, Loren Picco, Philipp Holliger, Lauren M. Oldfield, Andrew Hessel, and Thomas E. Gorochowski
Source/Credit: University of Bristol
Reference Number: bio040126_01University of Bristol
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