Evidence map›Paper›PMID 41398169›Full record

ArticleNature communications2025

Reconstituting transcription-translation-coupled DNA replication within complex in vitro biological systems.

Xiao Zheng, Wenli Gao, Wan-Qiu Liu, Yufei Zhang, Shuhui Huang, Xiangyang Ji, Yicong Lu, Yifan Liu, Shengjie Ling, Jian Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Xiao ZhengSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.ORCID http://orcid.org/0009-0005-1085-0900
Wenli GaoSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.ORCID http://orcid.org/0009-0001-2791-1192
Wan-Qiu LiuSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
Yufei ZhangSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
Shuhui HuangSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
Xiangyang JiSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
Yicong LuSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
Yifan LiuSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China.ORCID http://orcid.org/0000-0002-2989-6280
Shengjie LingSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China. lingshj@shanghaitech.edu.cn.ORCID http://orcid.org/0000-0003-1156-0479
Jian LiSchool of Physical Science and Technology, ShanghaiTech University, Shanghai, China. lijian@shanghaitech.edu.cn.ORCID http://orcid.org/0000-0003-2359-238X

Funding

National Natural Science Foundation of China (National Science Foundation of China) 32571664National Natural Science Foundation of China (National Science Foundation of China) 52322305
6 · The paper itself

Abstract

Reconstructing transcription-translation-coupled DNA replication (TTcDR) in artificial systems is crucial for creating synthetic life; however, existing approaches face limitations mainly due to their reliance on purified biological components. Here, we introduce LoopReX, a cell-free system that reconstitutes TTcDR using crude Escherichia coli extracts, offering a more complex native biological environment. LoopReX leverages a minimal machinery composed of phi29 DNA polymerase and T7 RNA polymerase, with the latter facilitating DNA replication initiation through the generation of primer RNAs. Using machine learning, we optimize LoopReX to enhance the efficiency of both DNA replication and protein expression, achieving scalable, sustainable genetic flow and high-yield protein production with robust iterative performance. Furthermore, artificial nucleoids, autonomously formed through CipB-based compartmentalization, improve DNA spatial organization and support multiple biological functions. This work advances the construction of artificial life by reconstituting TTcDR within a single, scalable, and functionalized system, opening exciting possibilities for synthetic biology, biotechnology, and bio-hybrid applications.

Indexed as

DNA ReplicationProtein BiosynthesisTranscription, GeneticCell-Free SystemDNA-Directed DNA PolymeraseDNA-Directed RNA PolymerasesEscherichia coliSynthetic BiologyViral Proteinsbacteriophage T7 RNA polymeraseDNA-Directed DNA PolymeraseDNA-Directed RNA PolymerasesViral Proteins

Identifiers

PMID41398169
PMCPMC12796468

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.