Source 1primary paper2025MED
Toolkit/MagMboI
MagMboI
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
MagMboI is a photoactivatable split version of the type II restriction endonuclease MboI configured as a multi-component switch for light-controlled nuclease function. The supplied evidence indicates that an optimized variant, MagMboI-plus, produced stronger genome rearrangement activity than the original MagMboI in Saccharomyces cerevisiae.
Usefulness & Problems
Why this is useful
MagMboI is useful as a light-gated endonuclease platform for controlling genome rearrangement processes in yeast. The available evidence specifically supports its relevance to top-down genome engineering applications in Saccharomyces cerevisiae.
Source:
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
Problem solved
This tool addresses the need for inducible control over restriction-enzyme-driven genomic rearrangements during genome engineering. The cited study specifically frames this as optimization of a photoactivatable endonuclease for top-down genome engineering.
Published Workflows
AlphaFold3-guided optimization of a photoactivatable endonuclease for top-down genome engineering.
2025Objective: Optimize a photoactivatable restriction enzyme for light-controlled top-down genome engineering using AlphaFold3-guided structural redesign.
Why it works: The workflow uses structural modeling of the MagMboI-DNA complex to identify split-site changes expected to improve interface area, complex stability, and protein-DNA contacts, then tests whether those predicted improvements translate into in vivo activity under blue light control.
blue-light-induced heterodimerization restores nuclease activityincreased MagMboI-DNA interface areastrengthened protein-DNA contactspreserved alpha-helical integrityAlphaFold3 structural modelingcomparison of neighboring split-site variantsin vivo testing in Saccharomyces cerevisiae
Stages
- 1.AlphaFold3 modeling of the MagMboI-DNA complex(in_silico_filter)
This stage provides structure-based insight to guide redesign before experimental testing.
Selection: structural insights into interaction between MagMboI and its target DNA recognition sequence required for Mg2+-dependent DNA cleavage
- 2.Comparison of neighboring split-site variants(hit_picking)
This stage narrows candidate split designs to a redesigned variant predicted to improve structural and functional properties.
Selection: identification of an alternative split that increases interface area and enhances complex stability relative to the original construct
- 3.In vivo evaluation in Saccharomyces cerevisiae(confirmatory_validation)
This stage tests whether structure-guided redesign improves in vivo function and reveals tradeoffs not captured by structural prediction alone.
Selection: comparison of blue-light-activated DNA-cleavage activity and genomic rearrangements between MagMboI-plus and the original MagMboI construct
Steps
- 1.Model the MagMboI-DNA complex with AlphaFold3engineered nuclease modeled with a computation method
Obtain structural insight into how MagMboI interacts with its target DNA recognition sequence.
Structural modeling is performed first to guide redesign before selecting alternative split sites for experimental comparison.
- 2.Compare neighboring split-site variants to identify an alternative splitoriginal construct and redesigned variant
Identify a split-site redesign predicted to improve interface area, stability, and protein-DNA contacts.
Variant comparison follows structural modeling because the model provides the rationale for which split-site changes may improve the construct.
- 3.Test MagMboI-plus in Saccharomyces cerevisiae under blue light activationredesigned variant benchmarked against original construct
Determine whether the redesigned variant improves in vivo DNA-cleavage activity and assess genome rearrangement consequences.
In vivo testing is done after redesign selection to confirm whether predicted structural improvements translate into useful cellular performance and to detect liabilities.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Target processes
recombinationInput: Light
Implementation Constraints
The current description states that MagMboI is derived from split MboI fragments fused to blue-light-inducible dimerization modules, implying a multi-component construct design. However, the supplied evidence does not specify the dimerization domains, expression strategy, cofactor requirements, or illumination conditions.
Evidence is limited to a single comparative claim from one 2025 study, with no independent replication in the supplied material. The record does not provide quantitative activity data, illumination parameters, off-target effects, fragment architecture, or validation outside Saccharomyces cerevisiae.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Observations
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
mixedYeastapplication demoSaccharomyces cerevisiae
Inferred from claim c6 during normalization. In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct. Derived from claim c6.
Source:
DNA-cleavage activity change(slightly increased)
Supporting Sources
Ranked Claims
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
genomic rearrangements more pronounced
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
DNA-cleavage activity change slightly increased
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
Approval Evidence
1 source6 linked approval claimsfirst-pass slug magmboi
Here, we report the AlphaFold3-guided enhancement of MagMboI, a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering. MagMboI is derived from the type II restriction enzyme MboI and functions through a split-protein strategy in which its N- and C-terminal fragments are fused to light-inducible dimerization modules. Upon exposure to blue light, these domains heterodimerize, restoring nuclease activity in a controlled manner.
Source:
comparative liabilitysupports
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
Source:
comparative performancesupports
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
Source:
general strategysupports
AlphaFold3-based prediction can accelerate functional improvements in engineered enzymes and provide a strategy for developing light-controlled genome engineering tools.
Source:
mechanismsupports
MagMboI functions through a split-protein strategy in which blue-light-induced heterodimerization restores nuclease activity.
Source:
structure guided designsupports
AlphaFold3 was used to model the MagMboI-DNA complex and provide structural insight into interaction with the 5'-GATC-3' recognition sequence required for Mg2+-dependent DNA cleavage.
Source:
tool descriptionsupports
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
Source:
Comparisons
Source-backed strengths
The supplied evidence supports that MagMboI can be improved, because MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI in Saccharomyces cerevisiae cells. This indicates functional tunability of the platform, but no quantitative performance metrics are provided in the supplied record.
Source:
MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells.
Source:
In Saccharomyces cerevisiae cells, MagMboI-plus showed slightly increased DNA-cleavage activity in vivo upon blue light activation compared with the original MagMboI construct.
Ranked Citations
- 1.