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PDMS Fabrication Protocol

  • Version: 1.0
  • Author: Mingchuan Tang
  • Last modified: 2025-10-30
  • Purpose: PDMS substrates for on-slide spatial transcriptomics reactions

Required Materials

  • PDMS: Sylgard 184 Silicone Elastomer Kit (Component A: base, Component B: curing agent)
  • Mold: 15 x 15 cm square mold
  • Other: Weighing container, stirring rod

Equipment

  • Balance (0.1g precision or better)
  • Vibrator/mixer
  • Vacuum pump and desiccator (for degassing)
  • Oven (80°C capable)
  • Blade or cutting tool

Formulation

  • Weight ratio: A:B = 10–12 : 1
  • Per batch: 120g total
    • Standard (10:1): A = 109.1g + B = 10.9g
    • Stiffer (12:1): A = 110.8g + B = 9.2g
  • Yield: 2 batches (240g) fill 3 molds (15 x 15 cm)

Steps

1. Weigh

  • Weigh Component A (base): 109.1–110.8g (depending on ratio)
  • Add Component B (curing agent): 10.9–9.2g
  • Total: 120g per batch

2. Mix

  • Pre-mix with stirring rod
  • Place on vibrator for thorough mixing: 5-10 min until uniform
  • Bubbles during mixing are normal

3. Degas

  • Transfer to vacuum desiccator
  • Apply vacuum for 15-30 min
  • Done when: no visible bubbles rising
  • Watch for overflow during degassing

4. Pour

  • Slowly pour degassed PDMS into mold
  • Pour from one side, let liquid self-level
  • Pop any remaining small bubbles with a needle
  • 2 batches (240g) = 3 molds

5. Cure

  • Place in oven at 80°C overnight (8-12 h)
  • Keep oven temperature stable; avoid opening door
  • Ensure mold is level

6. Demold & Cut

  • Cool to room temperature
  • Carefully peel cured PDMS from mold
  • Cut to required size with blade
  • Storage: Room temperature, long-term stable

Quality Check

  • Appearance: Transparent, colorless, smooth surface
  • Elasticity: Good elasticity, not easily torn
  • Bubbles: Minimal in surface and interior
  • Thickness: Uniform throughout

Troubleshooting

Problem Cause Solution
Sticky, doesn't set Inaccurate ratio or poor mixing Ensure precise weighing and thorough mixing
Too many bubbles Insufficient degassing Extend vacuum time or degas in stages
Uneven thickness Mold not level or poured too fast Level mold, pour slowly, gently tilt to spread
Incomplete curing Temperature or time insufficient Extend curing time or increase temp (max 100°C)

Notes

  • Components A and B should be at room temperature before mixing
  • Mix in well-ventilated area
  • Wear gloves; avoid skin contact with uncured PDMS
  • Cured PDMS can be autoclaved (121°C, 20 min)
  • Clean cutting tools to avoid contamination
  • Clean PDMS surface with ethanol or isopropanol before use

Curing Reference

  • Room temperature: 24 h
  • 80°C: overnight
  • 100°C: 2 h
  • Standard ratio (10:1): moderate hardness and elasticity
  • Higher ratio (12:1): harder, more brittle, better transparency