Ends Dec 1, PT
SciFig
Get Started Free

Gibson Assembly Diagram — Free Mechanism Editor

Keep overlaps, 3′ overhangs, internal gaps and repaired junctions consistent across an assembly explanation.

Gibson assembly diagram editor

Describe what you need in the box above.

Start with up to 150 free credits|No credit card required

Get up to 250 free credits on day one when you join through an invite.

3 figure engines · 500+ templatesEvery label editable · 60+ color schemesEditable PPTX · Layered SVG · 8K PNG / JPG

Gibson Assembly Diagram — Free Mechanism Editor— templates & examples

Updated

Free scientific tools

Gibson Assembly Diagram — Free Mechanism Editor

Keep overlaps, 3′ overhangs, internal gaps and repaired junctions consistent across an assembly explanation.

A Gibson assembly diagram explains how overlapping DNA fragments are joined through exonuclease treatment, annealing, polymerase filling and ligation. SciFig provides an editable teaching schematic of those stages, with defined strand direction and corresponding labels. Choose a mechanism stage and adapt its component names without changing the defined strand relationships. Create a labeled reference or a numbered exercise, export SVG or PNG, and save the current stage as a project.

Explore the assembly stages
Overlapping DNA fragments compared with the annealing stage and internal gaps
  • Begin with overlapping DNA fragments
  • Explain the 5′ exonuclease step
  • Compare annealing and repair
  • Export a mechanism teaching set

From Overlaps to Joined Strands

Follow strand direction and enzyme action through overlapping, resected, annealed and repaired views.

Begin with overlapping DNA fragments

The starting view shows three double-stranded fragments with terminal overlap regions. The strands run antiparallel, with separate labels for their 5′ and 3′ ends. These are teaching fragments rather than a submitted DNA sequence, so the picture can concentrate on orientation and the role of the shared terminal regions. Gibson assembly cloning uses terminal overlaps between adjacent fragments.

  • Three double-stranded fragments
  • Antiparallel end labels
  • Visible overlap regions
Explore overlapping fragments

Explain the 5′ exonuclease step

The exonuclease view removes material from the 5′ ends and leaves 3′ single-stranded extensions. The end anchors move to the remaining strand endpoints in that view. A separate overhang marker helps distinguish the exposed extension from the original fully double-stranded overlap. The Gibson assembly mechanism begins with 5′ resection that exposes complementary 3′ overhangs.

  • 5′ end resection
  • 3′ overhangs
  • Stage-specific end positions
Examine exonuclease resection

Compare annealing and repair

Complementary overlap regions align in the annealing view, with internal gaps still visible. The repair view fills those gaps from available 3′ ends and marks sealed junctions. The two views have different geometry, making polymerase filling and ligase sealing visible stages of the mechanism.

  • Complementary overlap pairing
  • Internal gaps after annealing
  • Gap filling and nick sealing
Compare annealing and repair

Export a mechanism teaching set

Switch among the starting fragments, exonuclease, annealing and repair views. Each supports labeled, numbered, blank and answer modes. Move the text labels, export SVG or PNG, and save the current project to restore its stage and annotation settings.

  • Four mechanism stages
  • Four annotation modes
  • SVG, PNG and JSON projects
Prepare the mechanism set

How to Illustrate the Assembly Stages

Choose the mechanism stage, edit its labels and export a reference, exercise or corresponding answer.

  1. Choose the structure or stage

    Open the local editor and start with its labeled view. For an experiment or mechanism with multiple stages, choose the condition that matches the explanation you are preparing.

  2. Edit the structure labels

    Select a part, edit its name and move the label endpoint with the pointer or coordinate controls. Its structure anchor stays attached to the defined component.

  3. Prepare the practice version

    Switch to numbered, blank or answer mode as needed. The practice figure and its answer list use the same part order for the selected structure or stage.

  4. Download or save the project

    Download SVG or PNG from the current valid figure. Save project JSON when you want to restore the labels, positions and display mode for another session.

Assembly Figures for Molecular Biology

Use the strand mechanism for cloning introductions, orientation exercises and protocol illustrations.

Gibson assembly diagram: overlap fragments

Molecular cloning introduction

Use the four stages to introduce the roles of exonuclease, polymerase and ligase. Identify the strand ends before explaining which end is resected or extended.

Explore this example
Gibson assembly diagram: exonuclease overhangs

DNA assembly mechanism slide

Place annealing and repair exports beside each other. Use the visible internal gaps and filled junctions to explain the transition.

Explore this example
Gibson assembly diagram: annealing gaps

Strand direction exercise

Export a numbered starting or exonuclease view and ask learners to identify 5′ ends, 3′ ends and overhangs. Match the answers to that selected stage.

Explore this example
Gibson assembly diagram: repaired junctions

Protocol overview illustration

Include a mechanism figure beside an assembly protocol. Keep experimental sequences, reagent amounts and incubation settings in the protocol itself.

Explore this example
Overlapping DNA fragments compared with the annealing stage and internal gaps

Plasmid planning discussion

Use this figure to explain how fragments join, then use a plasmid map to discuss the resulting circular construct and its features. The two figures serve different tasks.

Explore this example
Gibson assembly diagram: overlap fragments

Lab presentation figure

Rename the schematic fragments and export vector artwork for a presentation. Save the project to preserve the chosen mechanism stage and label placement.

Explore this example

Worked Examples Prepared with SciFig

The starting Gibson assembly diagram shows three double-stranded fragments with terminal overlap regions. I kept the strand-end labels visible to establish antiparallel orientation before the enzyme steps. The figure is a mechanism example, so the colored fragments communicate direction and overlap without implying sequence validation.

SciFig · Overlapping fragments

Figure preparation · SciFig

Free tools

A tool for every scientific figure

150 focused generators for the scientific figure you need — each opens in the right workspace with a matching example.

Illustrations, structures and concept diagrams

83 tools
Chemistry Structure Generator example figureChemistry Structure GeneratorGraphical Abstract Maker example figureGraphical Abstract MakerFree Body Diagram Generator example figureFree Body Diagram GeneratorCircuit Diagram Maker example figureCircuit Diagram MakerAI Scientific Image Generator example figureAI Scientific Image GeneratorEditable 96-Well Plate example figureEditable 96-Well PlateLewis Dot Structure Generator example figureLewis Dot Structure GeneratorDNA Structure Diagram Generator example figureDNA Structure Diagram GeneratorWiring Diagram Maker example figureWiring Diagram MakerP&ID Diagram Generator example figureP&ID Diagram GeneratorScientific Poster Generator example figureScientific Poster GeneratorCladogram Maker example figureCladogram MakerFood Web Maker example figureFood Web MakerMedical Illustration Generator example figureMedical Illustration GeneratorPCR Diagram Generator example figurePCR Diagram GeneratorPPT Text to Visual Converter example figurePPT Text to Visual ConverterMitosis Diagram Generator example figureMitosis Diagram GeneratorDog Lymph Nodes Diagram — Free Label Editor example figureDog Lymph Nodes Diagram — Free Label EditorFlow of Cerebrospinal Fluid — Free Diagram Editor example figureFlow of Cerebrospinal Fluid — Free Diagram EditorAI Infographic Generator example figureAI Infographic GeneratorAnatomical Drawing Generator example figureAnatomical Drawing GeneratorAnimal and Plant Cell Comparison example figureAnimal and Plant Cell ComparisonAnimal Cell Diagram Generator example figureAnimal Cell Diagram GeneratorAntibody Structure Diagram Generator example figureAntibody Structure Diagram GeneratorApoptosis Diagram Generator example figureApoptosis Diagram GeneratorAutophagy Diagram Generator example figureAutophagy Diagram GeneratorBacteria Diagram Generator example figureBacteria Diagram GeneratorBlueprint Maker example figureBlueprint MakerBohr Model Maker example figureBohr Model MakerBrain Anatomy Diagram example figureBrain Anatomy DiagramCalvin Cycle Diagram Generator example figureCalvin Cycle Diagram GeneratorCarbon Cycle Diagram Generator example figureCarbon Cycle Diagram GeneratorCell Cycle Diagram Generator example figureCell Cycle Diagram GeneratorCell Membrane Diagram example figureCell Membrane DiagramCellular Respiration Diagram Generator example figureCellular Respiration Diagram GeneratorComplement System Diagram Generator example figureComplement System Diagram GeneratorCRISPR-Cas9 Diagram Generator example figureCRISPR-Cas9 Diagram GeneratorDNA Replication Diagram Generator example figureDNA Replication Diagram GeneratorEar Anatomy Diagram example figureEar Anatomy DiagramElectron Configuration Diagram Generator example figureElectron Configuration Diagram GeneratorElectron Transport Chain Diagram Generator example figureElectron Transport Chain Diagram GeneratorELISA Diagram Generator example figureELISA Diagram GeneratorEye Anatomy Diagram example figureEye Anatomy DiagramFoot Anatomy Diagram example figureFoot Anatomy DiagramGel Electrophoresis Diagram Generator example figureGel Electrophoresis Diagram GeneratorGene Regulation Diagram Generator example figureGene Regulation Diagram GeneratorGlycolysis Diagram Generator example figureGlycolysis Diagram GeneratorHeart Diagram example figureHeart DiagramImage to Editable SVG Converter example figureImage to Editable SVG ConverterImmune Checkpoint Diagram Generator example figureImmune Checkpoint Diagram GeneratorImmune Response Diagram Generator example figureImmune Response Diagram GeneratorInflammasome Diagram Generator example figureInflammasome Diagram GeneratorKrebs Cycle Diagram Generator example figureKrebs Cycle Diagram GeneratorLab Diagram Maker example figureLab Diagram MakerMeiosis Diagram Generator example figureMeiosis Diagram GeneratorMetabolic Pathway Diagram Generator example figureMetabolic Pathway Diagram GeneratorMicroscope Diagram example figureMicroscope DiagramMolecular Orbital Diagram Generator example figureMolecular Orbital Diagram GeneratorNitrogen Cycle Diagram Generator example figureNitrogen Cycle Diagram GeneratorPedigree Chart Maker example figurePedigree Chart MakerPhospholipid Diagram Generator example figurePhospholipid Diagram GeneratorPhosphorus Cycle Diagram Generator example figurePhosphorus Cycle Diagram GeneratorPhotosynthesis Diagram Generator example figurePhotosynthesis Diagram GeneratorPhylogenetic Tree Maker example figurePhylogenetic Tree MakerPhysics Vector Diagram Maker example figurePhysics Vector Diagram MakerPlant Cell Diagram Generator example figurePlant Cell Diagram GeneratorPlasmid Map Maker example figurePlasmid Map MakerProtein Synthesis Diagram Generator example figureProtein Synthesis Diagram GeneratorPunnett Square Maker example figurePunnett Square MakerRay Diagram Maker example figureRay Diagram MakerRNA Structure Diagram Generator example figureRNA Structure Diagram GeneratorScientific Color Palette Generator example figureScientific Color Palette GeneratorSignaling Pathway Diagram Generator example figureSignaling Pathway Diagram GeneratorSingle Line Diagram Generator example figureSingle Line Diagram GeneratorT-Cell Activation Diagram Generator example figureT-Cell Activation Diagram GeneratorWater Cycle Diagram Generator example figureWater Cycle Diagram GeneratorWestern Blot Diagram Generator example figureWestern Blot Diagram GeneratorFungal Cell Diagram — Free Labeled Yeast Editor example figureFungal Cell Diagram — Free Labeled Yeast EditorGibson Assembly Diagram — Free Mechanism Editor example figureGibson Assembly Diagram — Free Mechanism EditorHigh Pressure Homogenizer Working Principle — Free Diagram example figureHigh Pressure Homogenizer Working Principle — Free DiagramNeuron Diagram example figureNeuron DiagramSpinning Disk Confocal Optical Diagram example figureSpinning Disk Confocal Optical DiagramSwan Neck Flask Experiment — Free Diagram Editor example figureSwan Neck Flask Experiment — Free Diagram Editor

Statistical charts and graphs

34 tools
Bode Plot Generator example figureBode Plot GeneratorSpider Chart Maker example figureSpider Chart MakerKaplan-Meier Survival Curve example figureKaplan-Meier Survival CurveMulti-Layer Pie Chart Maker example figureMulti-Layer Pie Chart MakerBell Curve Generator example figureBell Curve GeneratorGantt Chart Generator example figureGantt Chart GeneratorBox Plot Generator example figureBox Plot GeneratorForest Plot Generator example figureForest Plot GeneratorVolcano Plot Generator example figureVolcano Plot GeneratorPareto Chart Maker example figurePareto Chart MakerScatter Plot Maker example figureScatter Plot MakerHeatmap Generator example figureHeatmap GeneratorAI Chart Generator example figureAI Chart GeneratorComparison Chart Maker example figureComparison Chart MakerSankey Diagram Generator example figureSankey Diagram GeneratorRadar Chart Generator example figureRadar Chart GeneratorHistogram Maker example figureHistogram MakerBar Chart Generator example figureBar Chart GeneratorCoordinate Plane Generator example figureCoordinate Plane GeneratorDot Plot Creator example figureDot Plot CreatorWater Heating Curve example figureWater Heating CurveIC50 Calculator & Dose-Response Curves example figureIC50 Calculator & Dose-Response CurvesImage DPI Calculator example figureImage DPI CalculatorTransverse Wave Diagram Generator example figureTransverse Wave Diagram GeneratorLine Chart Generator example figureLine Chart GeneratorMA Plot example figureMA PlotNumber Line Generator example figureNumber Line GeneratorFigure Checker example figureFigure CheckerScientific Graph Maker example figureScientific Graph MakerFree Serial Dilution Calculator — Volumes & Diagram example figureFree Serial Dilution Calculator — Volumes & DiagramSupply and Demand Graph Maker example figureSupply and Demand Graph MakerUpSet Plot Generator example figureUpSet Plot GeneratorWaterfall Chart Maker example figureWaterfall Chart MakerPlace Value Chart example figurePlace Value Chart

Flowcharts, frameworks and structure diagrams

33 tools
Conceptual Framework Generator example figureConceptual Framework GeneratorTheoretical Framework Generator example figureTheoretical Framework GeneratorSyntactic Tree Generator example figureSyntactic Tree GeneratorDichotomous Key Maker example figureDichotomous Key MakerSentence Diagram Generator example figureSentence Diagram GeneratorText to Diagram Generator example figureText to Diagram GeneratorPRISMA Flow Diagram Generator example figurePRISMA Flow Diagram GeneratorWorkflow Diagram Generator example figureWorkflow Diagram GeneratorTimeline Generator example figureTimeline GeneratorSynthesis Matrix Generator example figureSynthesis Matrix GeneratorER Diagram Generator example figureER Diagram GeneratorUML Diagram Generator example figureUML Diagram GeneratorTree Diagram Generator example figureTree Diagram GeneratorFishbone Diagram Generator example figureFishbone Diagram GeneratorNeural Network Diagram Generator example figureNeural Network Diagram GeneratorDecision Tree Generator example figureDecision Tree GeneratorSoftware Architecture Diagram Generator example figureSoftware Architecture Diagram GeneratorChemical Process Flow Diagram Maker example figureChemical Process Flow Diagram MakerCONSORT Flow Diagram Generator example figureCONSORT Flow Diagram GeneratorContext Diagram Creator example figureContext Diagram CreatorData Flow Diagram Generator example figureData Flow Diagram GeneratorExperimental Workflow Diagram example figureExperimental Workflow DiagramGenogram Maker example figureGenogram MakerGraphic Organizer Generator example figureGraphic Organizer GeneratorImage to Flowchart Converter example figureImage to Flowchart ConverterMermaid to PNG Converter example figureMermaid to PNG ConverterNetwork Diagram Generator example figureNetwork Diagram GeneratorOrg Chart Maker example figureOrg Chart MakerSequence Diagram Generator example figureSequence Diagram GeneratorState Diagram Generator example figureState Diagram GeneratorSwimlane Diagram Generator example figureSwimlane Diagram GeneratorUse Case Diagram Generator example figureUse Case Diagram GeneratorVenn Diagram Generator example figureVenn Diagram Generator
Browse all tools →

Diagram and Export Questions

1.

2.

3.

4.

5.

6.

Call to action background

Create with SciFig

Gibson Assembly Diagram — Free Mechanism Editor

Explore the assembly stages

Free to start · No credit card required · Built for researchers