Last updated: April 21, 2026
Should You Use Array-Based or Column-Based Oligo Synthesis?
Use this page when you need to choose the right synthesis approach before ordering. It compares scale, full-length yield, error rate, purification, cost, and downstream handlingso you can decide whether array-based or column-based synthesis fits your project.
Array-based synthesis utilizing piezoelectric inkjet technology.
Array vs. Column: Which Fits Your Use Case?
| Feature | Array-Based (Pool) | Column-Based (Individual) |
|---|---|---|
| Parallelism | 1K-1M oligos simultaneously | 1 oligo per column (96-384 parallel) |
| Scale/Oligo | fmol-pmol (requires PCR) | 10-1000 nmol (use directly) |
| Coupling Efficiency | 98.5-99.5% per step | 99.0-99.8% per step |
| Error Rate | ~1 per 200 bases | ~1 per 500 bases |
| Full-Length (100-mer) | 30-60% | 70-95% |
| Max Length | 200-350 nt | 100-200+ bp |
| Cost/Oligo | Significantly lower | $5-50 |
| Purification | Pool-level only | HPLC, PAGE per oligo |
| Turnaround | 2-6 business days | 1-3 days |
| Best For | Libraries, pools, high-throughput | Primers, probes, critical sequences |
Which Array Platform Are You Ordering From?
| Technology | Vendor | Mechanism | Capacity | Max Length |
|---|---|---|---|---|
| Silicon-Based Array | Twist Bioscience | Silicon wafer with micro-wells, enzymatic cleavage | Min 2K oligos | 300 nt |
| Inkjet Printing | Agilent SurePrint | Piezoelectric jetting of reagents onto glass slides | Up to 244K/chip | 230 nt |
| CMOS Chip | GenScript GenTitan | CMOS-based electrochemical synthesis on semiconductor chip | Up to 8M/chip | 170 nt |
| Photolithographic | Affymetrix/legacy | UV light through photomasks for deprotection | Up to 1M | ~100 bp |
How Coupling Efficiency Changes Full-Length Yield
Full-length % = (Coupling Efficiency)^(N-1) × 100
| Oligo Length | 98.5% (Low Array) | 99.0% (Good Array) | 99.5% (Best Array) | 99.8% (Column) |
|---|---|---|---|---|
| 50-mer | 47% | 61% | 78% | 90% |
| 100-mer | 22% | 37% | 61% | 82% |
| 150-mer | 10% | 22% | 47% | 74% |
| 200-mer | 5% | 13% | 37% | 67% |
| 300-mer | 1% | 5% | 22% | 55% |
Use our Error Rate Calculator to compute full-length % for your specific oligo length.
Frequently Asked Questions
What is the fundamental difference between array and column synthesis?▾
Column synthesis builds one oligo at a time on glass beads (10-1000 nmol scale, high purity). Array synthesis uses a flat surface to build thousands-millions of different oligos simultaneously (fmol-pmol per oligo, lower purity but massively parallel). Both use phosphoramidite chemistry but differ in scale and addressability.
Why are array-synthesized oligos lower quality?▾
Three factors: (1) smaller synthesis scale means fewer molecules per sequence, amplifying stochastic failures; (2) surface-based coupling is less efficient (98.5-99.5% vs 99-99.8%); (3) less stringent purification since individual oligo purification is impossible in pools. However, this quality is sufficient for most pool applications.
Can array-synthesized pools be used for cloning?▾
Yes, routinely. After PCR amplification and error correction (optional), array oligo pools are cloned into vectors for CRISPR libraries, gene assembly, and variant libraries. Post-cloning sequence verification identifies correct clones.
Next Pages to Open
Read Oligo Pool QC Metrics
Uniformity, error rate, and Gini deep dive.
Check Oligo Pool Design Rules Before Ordering
Review sequence constraints that keep pools synthesis-ready.
Compare Oligo Pool Vendors
Twist vs Agilent vs IDT vs GenScript.
Order an Oligo Pool
File formats, ordering, delivery.
Design an Oligo Pool Before Ordering
Complete beginner guide.
Estimate Oligo Pool Cost Before Requesting Quotes
Estimate pricing by application before you contact vendors.