biocrnpyler.mechanisms.integrase

Classes

BasicIntegration([name, mechanism_type])	Basic DNA integration mechanism without enzyme involvement.
EnzymeIntegration([name, mechanism_type, ...])	Enzyme-catalyzed DNA integration mechanism with integrase.

class biocrnpyler.mechanisms.integrase.BasicIntegration(name: str = 'basic_integration', mechanism_type: str = 'integration', **kwargs)

Basic DNA integration mechanism without enzyme involvement.

An ‘integration’ mechanism that models the direct recombination or integration of two DNA molecules to form two new DNA products. This represents a simplified integration process without explicit enzyme involvement, useful for modeling the overall effect of site-specific recombination.

The integration reaction is given by

DNA1 + DNA2 –> DNA3 + DNA4

where DNA1 and DNA2 are input DNA molecules, and DNA3 and DNA4 are the recombined product DNA molecules.

Parameters:

namestr, default=’basic_integration’

Name identifier for this mechanism instance.

mechanism_typestr, default=’integration’

Type classification of this mechanism.

**kwargs

Additional keyword arguments (unused, maintained for API compatibility).

Attributes:

namestr

Name of the mechanism instance.

mechanism_typestr

Type classification (‘integration’).

See also

EnzymeIntegration

Integration with explicit integrase enzyme.

Mechanism

Base class for all mechanisms.

Notes

This mechanism generates a single irreversible mass-action reaction representing the overall integration process. It does not model the detailed molecular mechanism involving integrase binding or intermediate complexes.

Common applications include:

• Simplified models of site-specific recombination

• DNA rearrangement in synthetic biology circuits

• Cassette exchange systems

• Genome editing with minimal mechanistic detail

Required parameters for this mechanism:

• ‘kint’ : Integration rate constant

The mechanism does not generate new species (returns empty list from update_species) as it models the direct conversion without intermediate complexes.

Examples

See ‘Specialized_Tutorials/Integrase_Examples’.

update_reactions(DNA_inputs, DNA_outputs, component=None, part_id=None, kint=None, **kwargs)

Generate integration reaction for basic integration.

Creates a single irreversible mass-action reaction for DNA integration.

Parameters:

DNA_inputslist of Species

List of input DNA species to be integrated (typically 2).

DNA_outputslist of Species

List of output DNA species after integration (typically 2).

componentComponent, optional

Component containing parameter values. Required if kint is not provided directly.

part_idstr, optional

Identifier for parameter lookup. If None, defaults to component.name.

kintParameter or float, optional

Integration rate constant. If None, retrieved from component parameters.

**kwargs

Additional keyword arguments (unused).

Returns:

list of Reaction

List containing a single irreversible mass-action reaction: DNA_inputs –> DNA_outputs.

Raises:

ValueError

If component is None and kint is not provided.

Notes

The reaction follows simple mass-action kinetics with rate constant ‘kint’. All input DNA species are consumed and all output DNA species are produced simultaneously.

update_species(DNA_inputs, DNA_outputs=None, **kwargs)

Generate species for basic integration.

This method returns an empty list as basic integration does not create intermediate species or complexes.

Parameters:

DNA_inputslist of Species

List of input DNA species to be integrated.

DNA_outputslist of Species, optional

List of output DNA species after integration. Not used in species generation.

**kwargs

Additional keyword arguments (unused).

Returns:

list

Empty list (no new species generated).

Notes

This mechanism does not generate intermediate complexes. If modeling with explicit integrase-DNA complexes is needed, consider using a binding mechanism in combination with integration, or use the EnzymeIntegration mechanism.

class biocrnpyler.mechanisms.integrase.EnzymeIntegration(name: str = 'enzyme_integration', mechanism_type: str = 'integration', integrase='Int1', **kwargs)

Enzyme-catalyzed DNA integration mechanism with integrase.

An ‘integration’ mechanism that models site-specific recombination catalyzed by integrase enzymes. The mechanism explicitly includes the integrase as a catalyst that facilitates DNA recombination but is not consumed in the reaction. This mechanism uses tetrameric integrase complexes (4 integrase molecules) to catalyze the integration.

The integration reaction is given by

4*Int + DNA1 + DNA2 –> 4*Int + DNA3 + DNA4

where Int is the integrase enzyme, DNA1 and DNA2 are input DNA molecules, and DNA3 and DNA4 are the recombined product DNA molecules.

Parameters:

namestr, default=’enzyme_integration’

Name identifier for this mechanism instance.

mechanism_typestr, default=’integration’

Type classification of this mechanism.

integrasestr, default=’Int1’

Name of the integrase enzyme. A Species with this name and material_type ‘protein’ is created automatically.

**kwargs

Additional keyword arguments (unused, maintained for API compatibility).

Attributes:

integraseSpecies

The integrase enzyme species with material_type ‘protein’.

namestr

Name of the mechanism instance.

mechanism_typestr

Type classification (‘integration’).

See also

BasicIntegration

Integration without explicit enzyme.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models site-specific recombination with explicit integrase involvement. The integrase acts as a true catalyst, appearing on both sides of the reaction and not being consumed.

The mechanism uses 4 integrase molecules to model the tetrameric integrase complex typically formed during site-specific recombination (e.g., lambda phage integration, Cre-loxP recombination). This reflects the biological reality where integrase monomers form tetramers to catalyze strand exchange.

Common applications include:

• Lambda phage integration/excision systems

• Cre-loxP recombination

• FLP-FRT site-specific recombination

• Detailed models of integrase-mediated genome editing

Required parameters for this mechanism:

• ‘kint’ : Integration rate constant

The stoichiometry of 4 integrase molecules reflects biological integrase mechanisms where a tetramer is the active form. The mechanism does not generate intermediate complexes (returns empty list from update_species).

Examples

See ‘Specialized_Tutorials/Integrase_Examples’.

update_reactions(DNA_inputs, DNA_outputs, component=None, part_id=None, kint=None, **kwargs)

Generate integration reaction with integrase enzyme.

Creates a single irreversible mass-action reaction for enzymatic DNA integration with tetrameric integrase complex.

Parameters:

DNA_inputslist of Species

List of input DNA species to be integrated (typically 2).

DNA_outputslist of Species

List of output DNA species after integration (typically 2).

componentComponent, optional

Component containing parameter values. Required if kint is not provided directly.

part_idstr, optional

Identifier for parameter lookup. If None, defaults to component.name.

kintParameter or float, optional

Integration rate constant. If None, retrieved from component parameters.

**kwargs

Additional keyword arguments (unused).

Returns:

list of Reaction

List containing a single irreversible mass-action reaction: 4*integrase + DNA_inputs –> 4*integrase + DNA_outputs.

Raises:

ValueError

If component is None and kint is not provided.

Notes

The reaction includes 4 integrase molecules on both sides, modeling the tetrameric integrase complex required for site-specific recombination. The integrase is not consumed (acts as a true catalyst).

The stoichiometry reflects biological mechanisms like:

• Lambda integrase (Int) tetramer formation

• Cre recombinase synaptic complex

• Other integrase family enzymes requiring multimers

update_species(DNA_inputs, DNA_outputs=None, **kwargs)

Generate species for enzyme integration.

This method returns an empty list as enzyme integration does not create intermediate species or complexes in this implementation.

Parameters:

DNA_inputslist of Species

List of input DNA species to be integrated.

DNA_outputslist of Species, optional

List of output DNA species after integration. Not used in species generation.

**kwargs

Additional keyword arguments (unused).

Returns:

list

Empty list (no new species generated).

Notes

This mechanism does not generate intermediate integrase-DNA complexes. The integrase-DNA binding and tetramerization steps are implicitly captured in the overall rate constant ‘kint’. For more detailed mechanistic models, consider using explicit binding mechanisms before integration.