Introduction
Order linear DNA from Twist Bioscience directly from a Benchling notebook entry. The Twist app brings sequence analysis, feasibility checks, quote generation, and checkout into Benchling, so you can submit an order against the same sequences and entry you used to design the construct.
Who this is for: Scientists ordering gene fragments from Twist Bioscience as part of their Benchling workflow.
What you can do today:
- Submit one sequence at a time, or a worklist of sequences
- Get feasibility, complexity, and pricing from Twist before ordering
- Select delivery format (tube or plate), buffer, normalization, capping, and shipping address
- Pay with a Twist blanket PO
- Download a quote PDF and order confirmation
Before you start
You will need:
- The Twist Gene Fragments app installed on your tenant. If you do not see the app available, contact your Benchling POC.
- A Twist account, using the same email address as your Benchling account. The Twist Gene Fragments app authenticates you as the individual placing the order, so the email on both accounts must match.
- At least one shipping address configured in your Twist account. The app pulls shipping addresses from Twist; if none are set up, you will see a warning during checkout.
- A blanket PO with Twist for payment. If your team uses a different payment method, contact your Benchling POC
Place an order
You can insert the Twist app Canvas into any notebook entry. If this is your first order, your administrator may also provide a notebook template that includes the Canvas and step-by-step instructions.
Step 1: Insert the Twist app Canvas
- Open the notebook entry where you want to place the order.
- Click Insert and select the Twist app Canvas.
- Wait a few seconds for the Canvas to load. The Canvas header displays TwistCanvas.
Step 2: Add sequences
The Linear DNA Ordering page provides three input methods. Use only one per order.
Option A — Search for individual sequences: Use the Search for DNA Sequences field to add sequences one at a time.
Option B — Select a worklist: Use the Or select a Worklist field to add a worklist of sequences. This is the faster path for bulk orders.
Option C — Paste nucleotide strings: Use the Or add sequences as nucleotide strings section to paste raw nucleotides. For each sequence:
- Enter a name in Sequence Name.
- Paste the nucleotides into Sequence Nucleotides.
- Use Add Rows to add more sequences, or Clear All to start over.
Note: Benchling sequence names will be used as construct names submitted to Twist. Names longer than 35 characters will be truncated. If names duplicate after truncation, an index will be appended (for example,
_1,_2).
Note: Worklists accept unique sequences only. If you need the same sequence in multiple positions, this is not supported in the current release.
Step 3: Select adapter preference
Below the input section, set the Adapters dropdown. The app defaults to No (without adapters). Change to Yes if you want to order with adapters.
Step 4: Authenticate to Twist (first time only)
The first time you use the app, you will be prompted to authenticate to your Twist account. Authentication lasts a few days; you will not need to re-authenticate for every order.
- After you select sequences and click Analyze Sequences for the first time, the Canvas displays Authentication Required.
- Click the Twist Account Authentication link.
- Sign in to Twist through Okta with your email and password.
- You will see Authentication successful! You can return to Benchling. Return to the Benchling tab.
- You may have to wait a minute or so for your Benchling Canvas to refresh and acknowledge the authentication
- Click Analyze Sequences again to continue.
Step 5: Analyze sequences
Click Analyze Sequences. The app sends the sequences to Twist's API and shows Analyzing sequences for feasibility… while it works.
Note: When the Canvas is processing an API call, it pauses briefly. This is normal. If it remains frozen for more than 5–10 minutes, reload the notebook entry or contact Benchling Support.
Step 6: Review feasibility and pricing
The Review & Pricing page shows a table of every sequence with its analysis results:
- Name — your Benchling sequence name (truncated to 35 characters if longer)
- Sequence — first nucleotides of the sequence
- BP — number of base pairs
- GC % — overall GC content
- Complexity Score — Standard, Complex, or Not Accepted
- Price (USD) — based on your Twist contract
- Feasibility — green dot (feasible) or red dot (infeasible)
Feasibility key:
| Indicator | Meaning | What to do |
|---|---|---|
| 🟢 Green dot | Feasible. Will be included in your order. | Continue. |
| 🔴 Red dot | Infeasible. Twist cannot synthesize this sequence as written. | The sequence will be excluded automatically from your order. To order infeasible sequences, contact customersupport@twistbioscience.com. To make the sequence feasible, edit it in Benchling and re-run the analysis. |
Warnings and errors: Below the table, the Warnings & Errors section shows a count of warnings and errors. Click Show Issues to expand the full list. Each warning lists the sequence name and a description, such as high GC content, repeat density, repeat regions, or homopolymer stretches.
A sequence with warnings can still be ordered. To resolve a warning, edit the sequence in Benchling (for example, using codon optimization tools) and re-run the analysis.
When you are ready, click Continue → to move to order settings.
Step 7: Configure your order
The configuration flow walks through five settings, one screen at a time. Each screen shows your progress at the top: completed selections have a green checkmark ✅, the current step has a blue arrow ⬆, and upcoming steps show an hourglass ⏳.
Screen 1: Delivery Format Choose how Twist ships your DNA. Options shown reflect what Twist currently offers.
Note: Plates are filled By Column. Custom plate maps that assign specific sequences to specific wells are not supported in the current release.
Screen 2: Shipment
Screen 3: Buffer
Screen 4: Normalization Choose:
Screen 5: Capping Capping is only available when Normalization is set to No.
- When normalization is set to Yes, capping is skipped automatically.
Step 8: Review the Order Summary and request a quote
The Order Summary page displays every selection you made: Delivery Format, Shipment, Buffer, Normalization, and Capping. Review them carefully — if you need to change anything, use the Back button.
Under Shipping Address, you will see the addresses configured on your Twist account. Click Use next to the address you want.
When you are ready, click Request Quote → to retrieve final pricing from Twist.
Step 9: Checkout
The Checkout page shows:
- Order Summary — repeats your selections
- Pricing Breakdown — Item Subtotal, Shipping, Handling, and Total Cost. Detailed line items break out price by sequence length band (e.g. 300bp–500bp, 501bp–1800bp).
- Download Quote PDF — click to download a PDF of the quote
- Payment Method — your blanket POs from Twist
Click Use next to the blanket PO you want to use, then click 🛒 Place Order Now.
Step 10: Order confirmation
After placing the order, the Canvas shows the Order Confirmation page with:
- Quote Number (for example, Q-451959)
- Status (ORDER_CREATED)
- Order Total
- Payment method
- Full order details
- What Happens Next? — production timeline (2–4 business days), including queuing, manufacturing and QC, and shipping
- Contact information for Twist customer support
-
You will receive — list of expected communications:
- Order confirmation email (within 1 hour)
- Production updates (weekly)
- Shipping notifications (when ready)
- Final delivery confirmation
Save your Quote Number for future reference. The Canvas persists in your notebook entry, so you can return to the confirmation any time.
After you order
- Order status, shipment tracking, and updates happen in Twist. You will receive email updates from Twist about production, QC, and shipment status. The Twist app does not currently surface these updates inside Benchling.
- The Canvas persists in your notebook entry. You can revisit your order configuration and confirmation any time, as long as you do not delete the Canvas.
- To place another order, insert a new Canvas in a notebook entry. Each order is tracked independently.
- Returned DNA preps are not automatically registered in Benchling in this release. Register preps using your existing process when the order arrives.
FAQ and known limitations
Can I order the same sequence in multiple positions in a plate? Not in this release. Worklists accept unique sequences only, and custom plate maps are not supported.
Can I order clonal genes or antibodies? Not through this app today. The current release supports linear DNA (gene fragments) only.
Can I upload a custom plate map? Not in this release. If you select a plate delivery format, sequences fill the plate By Column in the order Twist receives them.
How do I order without adapters? The Adapters dropdown on the Linear DNA Ordering page defaults to No. Change it to Yes if you want to order with adapters.
Can I export a list of sequences that failed feasibility? Not in this release. If your worklist contains many failures, you will need to scroll through the analysis table to identify them.
Can I order an infeasible sequence anyway? Not through the app. The app excludes infeasible sequences from the order automatically. Contact Twist customer support at customersupport@twistbioscience.com to discuss exceptions.
How long does authentication last? Authentication lasts a few days. You will not need to re-authenticate for every order.
Why did the Canvas freeze? The Canvas pauses while it makes API calls to Twist. This is normal. Give it 5–10 minutes. If it does not recover, reload the notebook entry or contact Benchling Support.
My sequence name was truncated. Why? Twist construct names are limited to 35 characters. Names longer than that are truncated. If two truncated names match, the app appends an index (_1, _2).
Where do I find the construct name Twist will use? The Name column on the Review & Pricing page shows the name as it will be submitted to Twist, after any truncation or indexing.
Who do I contact for help?
- Order, pricing, or Twist account issues: customersupport@twistbioscience.com
- Benchling app or interface issues: support@benchling.com