Source 1primary paper2025MED
Toolkit/MagMboI-plus
MagMboI-plus
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
MagMboI-plus is a redesigned photoactivatable endonuclease variant used as a light-controlled multi-component switch in Saccharomyces cerevisiae. In vivo, blue-light activation yields slightly increased DNA-cleavage activity relative to the original MagMboI construct, but also more pronounced genomic rearrangements.
Usefulness & Problems
Why this is useful
This tool is useful for light-gated induction of DNA cleavage in yeast, enabling temporal control over genome engineering workflows linked to recombination. The available evidence indicates improved activity over the original MagMboI construct, while also highlighting a tradeoff in genome stability.
Source:
MagMboI is a photoactivatable restriction enzyme designed for light-controlled top-down genome engineering.
Problem solved
MagMboI-plus addresses the need for externally controllable endonuclease activity during top-down genome engineering in Saccharomyces cerevisiae. Specifically, it provides a photoactivatable route to trigger cleavage-associated recombination processes with light rather than constitutive nuclease action.
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.
Techniques
Computational DesignTarget processes
recombinationInput: Light
Implementation Constraints
The available evidence supports use in Saccharomyces cerevisiae and activation by blue light. No further practical details are provided here regarding cofactors, expression strategy, domain composition, or delivery format.
The same source reports that MagMboI-plus induced more pronounced genomic rearrangements than the original MagMboI construct in Saccharomyces cerevisiae cells. The supplied evidence does not provide quantitative performance metrics, detailed construct architecture, or validation outside yeast.
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 source5 linked approval claimsfirst-pass slug magmboi-plus
This redesigned variant (designated MagMboI-plus) preserves b1-helical integrity while strengthening protein-DNA contacts. Although MagMboI-plus, when introduced in Saccharomyces cerevisiae cells, exhibited slightly increased DNA-cleavage activity in vivo upon blue light activation, it was found to induce more pronounced genomic rearrangements compared to the original MagMboI construct.
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:
variant improvementsupports
An alternative split-site variant, MagMboI-plus, increases the MagMboI-DNA interface area and enhances complex stability relative to the original construct.
Source:
variant propertysupports
MagMboI-plus preserves alpha-helical integrity while strengthening protein-DNA contacts.
Source:
Comparisons
Source-backed strengths
The reported study describes MagMboI-plus as an optimized variant with slightly increased in vivo DNA-cleavage activity compared with the original MagMboI construct. It was evaluated in Saccharomyces cerevisiae in the context of top-down genome engineering, providing direct organism-level evidence for function.
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.