When configuring your system, selecting the correct bottle and cap type for your reagents and amidites is essential for proper plumbing, sealing, and operational performance. This guide provides an overview of the most common bottle cap types and when each should be used.
🧪 Reagent Bottle Cap Sizes
Reagent bottles typically come with one of the following cap sizes:
Common Cap Types:
- GL38 – Common in North America and other parts of the world that do not go by European standards. Widely used for bottles of 4 Liter size.
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GL45 – Widely used in Europe and considered a global laboratory standard. Widely used for bottles of 2.5 Liter size
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28-400 – Common globally and compatible with many off-the-shelf lab bottles. You will typically see this bottle size used for 250ml or 450ml bottles.
Choosing the Right Size:
- GL38 are more typical in North America. Recommended for ACN and Deblock in most instances. For High Volume instruments, such as H8VLS or H32, this might also be recommended for OXI, ACT, CAP A and CAP B
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GL45 is most often used in European labs or with reagent distributors that follow EU standards. You will typically see these bottles in 2.5 Liter Sizes. Recommended in instances where GL38 is not common.
- 28-400 are typical globally and used to house smaller volumes of a reagent. Recommended for OXI, ACT, CAP A, CAP B and thiolation reagents. In very small volume applications such as H2, S4, H4, this might also be suitable for Deblock.
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If you're unsure, please check with your reagent distributor to confirm the bottle and cap type prior to configuration.
🔄 Daisy-Chained Bottle Caps
In cases where higher reagent volumes are needed or where changing bottles mid-run is inconvenient, a Daisy-chained Bottle Cap can be used to connect two bottles of the same reagentf:
- This is only available for GL38 or GL45 bottles
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The bottles must use the same cap size
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Your system supports daisy-chaining (consult your technical manual or support rep)
Daisy-chaining is commonly used for ACN and Deblock bottles to extend reagent capacity between changeovers without changing plumbing setups.
🔄 Recommendations by Reagent
| Reagent Type | Usage | Recommended Bottle Size | Cap Type | Notes |
|---|---|---|---|---|
| ACN (Acetonitrile) | Most frequently used reagent | 2.5 L or 4 L | GL38 or GL45 | Daisy-chaining recommended for very High Scale applications (H8VLS, H32, Shasta) |
| Deblock | Second highest usage | 2.5 L or 4 L (or 450 mL for low use) | GL38, GL45, or 28-400 | Choose size based on synthesis volume |
| Other Standard Reagents | Used in lower volumes | 450 mL (or 2.5 L / 4 L for high output) | 28-400 (GL38/GL45 for large volume) | For H32, H8-VLS, or Shasta larger bottles will be needed |
| Auxiliary Reagents (“S”) | S1 typically used for sulfurization | Typically 450 mL | 28-400 | “S” positions not present on S4 or H32 models; use larger bottles only if needed |
🧬 Amidite Bottle Cap Sizes
Amidites are available in various bottle types based on usage scale, cost sensitivity, and handling needs. The 28-400 cap size is the most common and widely supported, but others are used in specific scenarios.
Common Bottle & Cap Configurations:
| Bottle Type | Volume Range | Typical Use | Amidite Scale | Image |
|---|---|---|---|---|
| 28-400 Bottles | 30–450 mL | Most common | Varies |  |
| Septum Bottles | 6.5–100 mL |
Specific Suppliers |
50 µmol to 5 g |  |
| 20-400 Bottles | 30–60 mL | Mid-scale prep | 50 µmol to 2 g |  |
| 4 mL Vials (20-400 Cap) | ~4 mL | Low-use or expensive modifiers | Trace to low µmol |  |
Choosing the Right Option:
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28-400: Best default choice if compatibility is not already specified.
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20-400: Used for medium-volume applications where septum bottles are not required.
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4 mL vials: Useful for modifiers or low-usage amidites to reduce waste and exposure.
- Septum bottles: Recommended based on the supplier for amidites
| Bottle Type | Bottle Cap Image |
|---|---|
| 28-400 Bottles |  |
| Septum Bottles |  |
| 20-400 Bottles |  |
| 4 mL Vials (20-400 Cap) |  |
✅ Final Recommendations
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Confirm bottle type, volume, and cap size with your reagent and amidite suppliers before finalizing your configuration.
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If you are placing a new order or configuring a new instrument, make sure to communicate these specifications to our team so we can build your system accordingly.
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Incompatibility between bottle types and plumbing setups may require additional adapters or limit system performance.
If you’re unsure which configuration is best for your application, feel free to contact our team — we’re happy to help guide you through it.