xGen® Blocking Oligos

xGen® Blocking Oligos prevent adapter cross hybridization and minimize off-target capture, increasing specificity during targeted sequencing.

xGen® Universal Blockers—TS Mix is designed for use with either Illumina dual- or single-index adapters. This ready-to-use mix effectively blocks Illumina barcoded adapters to significantly improve on-target performance.


  • Improve on-target performance by reducing adapter-to-adapter hybridization
  • Effectively block multiple barcoded adapters using a single set of blocking oligos
  • Reduce workflow steps with a convenient premixed liquid formulation

Also available

  • Blocking oligos Ion Torrent adapters
  • xGen® Standard Blocking Oligos
  • xGen® Custom Blocking Oligos
  • xGen Blocking Oligos for diagnostics—contact GMPinfo@idtdna.com for information
To order xGen Universal Blocking Oligos offered separately for dual- and single-index adapters, click here.


For Single-Index Adapters (e.g., Illumina TruSeq®)

Predesigned to bind to the most common single-index library adapters that comprise 1 universal adapter and 24 barcoded adapters. The 24 blocking oligos for the barcoded adapters are labeled 1–27, corresponding to the numbering scheme used in Illumina, NEB, and Bioo Scientific single-index adapter kits.

For Dual-Index Adapters (e.g., Illumina TruSeq® HT)

Designed to block Illumina TruSeq HT® dual-index adapters, i5 and i7. The i5 oligos consist of numbers D501–D508 and the i7 oligos consist of D701–D712.

For Ion Torrent Barcoded Adapters

Predesigned against 2 non-barcoded adapters (A and P1) and 32 barcoded A adapters.

For Roche/454 Adapters

Protocols for blocking Roche 454 GS and GS Jr adapters generally require only 2 blocking oligos. The adapters in this set are recommended by Roche Nimblegen in the SeqCap LR V3.0 protocol.

xGen® Standard Blocking Oligos


Custom Designs

10 nmole xGen® Blocking Oligo$0.99 USD / Base20 - 75 Bases
25 nmole xGen® Blocking Oligo$1.99 USD / Base20 - 75 Bases

Available Modifications and Services

Description10 nmole xGen® Blocking Oligo25 nmole xGen® Blocking Oligo
HPLC$70.00 USD$104.00 USD
3' C3 Spacer$55.00 USD$85.00 USD
3' Dideoxy-C$125.00 USD$194.00 USD
Int deoxyInosine$12.00 USD$18.00 USD

Custom Yield or Modification Quote

While we have identified the most commonly used modifications and services required for effective blocking in next generation sequencing, IDT understands that certain modifications or services may improve the performance of our oligonucleotides for your specific application. In the event that the standard modifications or yields do not meet your needs, please request a custom quote.

Note: If you have previously ordered your blocking oligos as custom oligos, you do not need to request a new quote. Simply add the custom blocking oligos to your cart from the order history in your online account.

xGen® Custom Blocking Oligos

xGen® Blocking Oligos

Prevent adapter cross-hybridization by using xGen Blocking Oligos in your target capture reactions. Adapter sequences specific to a given next generation sequencing platform are ligated to all library fragments, both on-target and off-target, before enrichment. These adapter sequences can hybridize with each other during enrichment, creating a "daisy-chain" effect in which off-target fragments are captured along with on-target fragments, which can impact sequencing efficiency.

xGen Blocking Oligos bind to platform adapter sequences on a designated strand (usually the inverse of the synthetic adapter) to help prevent non-specific binding. Blocking the adapter sequences significantly improves capture performance [1,2].

All xGen Blocking Oligos are compatible with any xGen Lockdown Panel or custom xGen Lockdown Probe set. Each oligo is individually synthesized and assessed by mass spectrometry for quality control. Predesigned xGen Universal Blockers receive additional functional validation to improve performance and provide consistent results.

xGen® Universal Blockers—TS Mix

xGen Universal Blockers—TS Mix is a specially formulated blend of IDT’s industry leading universal blocking oligos for Illumina adapters. Based on proprietary technology, this ready-to-use, single tube mix blocks Illumina LT (p5, p7- 6nt & 8nt) and HT (i5, i7) adapters to deliver optimal on-target sequencing performance and overall cost-effectiveness. Both 16- and 96-reaction formats are available for convenient experimental design and use with xGen Lockdown® Panels or xGen Lockdown Probe sets.

xGen Blocking Oligos for Ion Torrent Adapters

These universal blockers are specific to the P1 and barcoded A adapters.

xGen Standard Blocking Oligos

Standard blocking oligos are made-to-order oligonucleotides that target specified adapter sequences.

xGen Custom Blocking Oligos

Custom blocking oligos are available in either Universal or Standard formats.


  1. Blumenstiel B, Cibulskis K, et al. (2010) Targeted exon sequencing by in-solution hybrid selection. Curr Protoc Hum Genet, Chapter 18:Unit 18.4.
  2. Hodges E, Rooks M, et al. (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 4(6):960–974.

Enhance Capture Performance by Blocking Platform Adapters

Figure 1. Blocking Oligos Increase On-Target Read Percentage. Several published articles have shown markedly higher on-target percentage by adding oligo blockers. For example, Blumenstiel et al. [1] increased on-target reads from 35% to 59% by including blocking oligos before target capture; Hodges et al. [2] achieved even better performance with blocking oligos, improving their on target reads from 32% before blocking oligos to 64% after the addition of blocking oligos. This approximately two-fold increase in on-target reads allows for multiplexing of a greater number of samples and increases read depth for easier identification of rare alleles.

High and Low Throughput Options with Excellent Peformance

Figure2. A Single xGen® Universal Blocking Oligo Effectively Enhances Multiplex Sequencing. Blocking oligos improve on-target capture percentage by binding to adapter sequences to prevent cross-hybridization from occurring between library fragments. xGen Universal Blocking Oligos enhance performance and enable higher multiplexing by blocking multiple barcoded adapters using a single oligonucleotide sequence. The data show 4-plex sequencing of genomic DNA enriched using a 1.2 Mb xGen Lockdown® panel and run on an Illumina MiSeq® platform. The percent on-target includes a 500bp buffer region at each end of the target. Error bars indicate standard deviation.

Performance Guarantee

All products have been functionally tested using the xGen® Rapid Capture Protocol, which is available online. Please contact IDT at xgen@idtdna.com for more information on tested protocols. Products are expected to be functional for up to 6 months after the "sell by" date listed on the tube.