What is a Construct?

A construct is a designed genetic sequence in Kernel. Constructs represent plasmids, expression vectors, linear DNA fragments, or any engineered genetic element.

Construct Components

Sequence

The DNA sequence is the foundation of every construct. Sequences can be:

• Circular: Plasmids and circular vectors

• Linear: DNA fragments, cassettes, or linear vectors

Parts

Parts are functional elements mapped to sequence regions:

• Promoters driving expression

• Coding sequences (genes)

• Terminators ending transcription

• Origins of replication

• Selection markers

Annotations

Annotations label sequence features:

• Part annotations linked to part definitions

• Custom annotations for any feature

• Imported annotations from GenBank files

Construct Views

Kernel provides three ways to visualize constructs:

Schematic View

A symbolic representation showing parts as standardized icons:

• Parts arranged linearly

• Direction indicated by symbol orientation

• Part names labeled above

• Color-coded by part type

Sequence Viewer

The DNA sequence displayed with:

• Nucleotide letters (A, T, G, C)

• Position markers

• Annotation tracks below the sequence

• Selection highlighting

Circular Map

For circular constructs (plasmids):

• Parts arranged around a circle

• Size shown in the center (bp)

• Useful for visualizing plasmid organization

Construct Editor Views

Construct Properties

Basic Information

• Name: Identifies the construct

• Description: What the construct does

• Topology: Circular or linear

Metadata

• Repository: Where the construct is stored

• Created/Modified: Timestamps

• Created by: Author

Attributes

Custom fields for your workflow:

• Project name

• Organism/host

• Selection marker

• Any custom properties

Construct Groups

Construct groups link related constructs that work together. Common use cases:

Multi-Plasmid Systems

Antibodies with separate heavy and light chain plasmids:

• HC plasmid (heavy chain)

• LC plasmid (light chain)

Co-Transfection Sets

Multiple plasmids transfected together:

• Expression vector

• Helper plasmid

• Reporter construct

Creating a Group

1. Select multiple constructs

2. Right-click and select Group constructs

3. Name the group

4. Grouped constructs appear together in searches and views

Revisions

Kernel tracks construct history:

• Every save creates a revision

• View revision history in the History panel

• Compare changes between versions

• Revert to previous versions if needed

Next Steps

• Creating Constructs — Build new constructs

• Drag and Drop Assembly — Visual construct design

• Annotations — Label sequence features