Toolkit Items

Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.

4 items matching 1 filter

Mechanism Branch

Layer 1

Mechanisms

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Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.

Layer 2

Architectures

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Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.

Layer 3

Components

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Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.

Technique Branch

Layer 1

Approaches

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High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.

Layer 2

Methods

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Concrete methods used to design, build, verify, or characterize engineered systems.

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sequence-specific dna binding

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transcription activator-like effector nucleases

Construct Pattern
Since 2015double-strand dna cleavagePhotocleavagesequence-specific dna bindingComputational DesignDirected Evolution

Transcription activator-like effector nucleases (TALENs) are programmable site-specific nucleases used for genome editing. The supplied evidence describes them as artificial systems with customizable DNA-binding motifs that can be designed to target specific genomic loci, bind practically anywhere in the genome, and cleave double-stranded DNA.

CFBacMamMusHumTxRep
Ev 45Rep 31Pr 83

aureochrome-1

Protein Domain
Since 2021blue-light sensing by a lov domainlight-induced conformational changelight-induced signal transmission via the hydrophobic region of the lov β-sheet surfacesequence-specific dna bindingsignal transmission via the hydrophobic region of the lov β-sheet surface

Aureochrome-1 (AUREO1) is a blue-light receptor from Vaucheria frigida with an N-terminal bZIP DNA-binding domain and a C-terminal LOV photosensory domain. Full-length AUREO1 binds DNA in a sequence-specific manner, and light signaling is transmitted from the LOV core via the hydrophobic region of the LOV β-sheet surface.

CFBacMamMusHumTxRep
Ev 37Rep 20Pr 71

PORC promoter

RNA Element
Since 2014protein-protein interaction-dependent modulation of dna bindingsequence-specific dna bindingtranscriptional regulationFunctional Assay

The PORC promoter is an Arabidopsis promoter element that functions as an in vivo binding target of the scarecrow-like transcription factor SCL27. Available evidence indicates that SCL27 binds GT cis-elements within this promoter and regulates PORC promoter activity, with DELLA proteins reducing SCL27 promoter binding.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 71

TALE DNA-binding domain

Protein Domain
Since 2013light-controlled two-hybrid recruitmentreversible optogenetic control of transcriptionsequence-specific dna bindingtargeted epigenetic chromatin modification

The TALE DNA-binding domain was used in the LITE system as a customizable genomic targeting module within an optogenetic two-hybrid architecture that integrates cryptochrome 2 and CIB1. In this context, it directs light-responsive regulation of endogenous mammalian transcription and targeted epigenetic chromatin states at selected loci.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 59
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