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DNA/RNA Synthesis

Ultramer® Oligonucleotides

DNA Oligos up to 200 bases

IDT  proprietary synthesis systems and chemistries allow the high-fidelity synthesis of very long oligos (up to 200 bases). Ultramer Oligonucletides are suitable for demanding applications such as cloning, ddRNAi, and gene construction and can save researchers a great deal of time and trouble in these applications through direct synthesis of the entire target fragment.

Delivered in Tubes

4 nmole Ultramer® DNA Oligo$0.75 USD / Base45 - 200 BasesOrder
20 nmole Ultramer® DNA Oligo$1.50 USD / Base45 - 200 BasesOrder
PAGE Ultramer® DNA Oligo$0.75 USD / Base60 - 200 BasesOrder
Note: There is a purification fee of
$110.00 USD
for each PAGE Ultramer® DNA Oligo.

Delivered in Plates

200 picomole Ultramer® DNA Plate Oligo$0.15 USD / Base45 - 200 BasesOrder
4 nmole Ultramer® DNA Plate Oligo$0.40 USD / Base45 - 200 BasesOrder
20 nmole Ultramer® DNA Plate Oligo$0.80 USD / Base45 - 200 BasesOrder

Product Specifications

  • 45 to 200 bases (60 to 200 bases for PAGE-purified Ultramer oligos)
  • Delivered normalized and dried down in tubes or plates
  • Ideal for gene construction, cloning, and ddRNAi
  • Standard desalted Ultramer Oligonucleotides ship in 2–4 business days
  • PAGE-purified Ultramer Oligonucleotides ship in 4–7 business days

Ultramer Oligonucleotide Modifications

Delivered in Tubes

Description4 nmole Ultramer® DNA Oligo20 nmole Ultramer® DNA OligoPAGE Ultramer® DNA Oligo
5' Phosphorylation$20.00 USD$25.00 USD$25.00 USD
5' Biotin$50.00 USD$60.00 USD$60.00 USD
5' Amino Modifier C6$26.00 USD$32.00 USDN/A
5' Amino Modifier C12$55.00 USD$70.00 USDN/A
5' deoxyInosine$10.00 USD$12.00 USD$12.00 USD
5' deoxyUridine$10.00 USD$12.00 USD$12.00 USD
Int deoxyInosine$10.00 USD$12.00 USD$12.00 USD
Int deoxyUridine$10.00 USD$12.00 USD$12.00 USD
Phosphorothioate Bond$3.50 USD$3.50 USD$3.50 USD
2' O-Methyl RNA bases$8.50 USD$13.50 USD$13.50 USD
3' Ribo A$30.00 USD$40.00 USD$40.00 USD
3' Ribo C$30.00 USD$40.00 USD$40.00 USD
3' Ribo G$30.00 USD$40.00 USD$40.00 USD
3' Ribo U$30.00 USD$40.00 USD$40.00 USD
3' Amino Modifier$28.00 USD$35.00 USDN/A
5' 5-Methyl dC$50.00 USD$60.00 USD$60.00 USD
Int 5-Methyl dC$50.00 USD$60.00 USD$60.00 USD
3' Phosphorylation$25.00 USD$30.00 USD$30.00 USD
Int Spacer 18$50.00 USD$60.00 USD$60.00 USD
3' C3 Spacer$45.00 USD$55.00 USD$55.00 USD

Delivered in Plates

Description200 picomole Ultramer® DNA Plate Oligo4 nmole Ultramer® DNA Plate Oligo20 nmole Ultramer® DNA Plate Oligo
5' Phosphorylation$10.00 USD$10.00 USD$12.50 USD
5' Biotin$20.00 USD$20.00 USD$25.00 USD
5' Amino Modifier C6$12.00 USD$12.00 USD$17.50 USD
5' Amino Modifier C12$27.50 USD$27.50 USD$35.00 USD
5' deoxyInosine$4.00 USD$4.00 USD$5.00 USD
5' deoxyUridine$4.00 USD$4.00 USD$5.00 USD
Int deoxyInosine$4.00 USD$4.00 USD$5.00 USD
Int deoxyUridine$4.00 USD$4.00 USD$5.00 USD
Phosphorothioate BondInquire for Pricing$3.50 USD$3.50 USD
2' O-Methyl RNA bases$8.50 USD$8.50 USD$13.50 USD
3' Ribo AN/A$30.00 USD$40.00 USD
3' Ribo CN/A$30.00 USD$40.00 USD
3' Ribo GN/A$30.00 USD$40.00 USD
3' Ribo UN/A$30.00 USD$40.00 USD
3' Amino ModifierN/A$28.00 USD$35.00 USD
5' 5-Methyl dCN/A$50.00 USD$60.00 USD
Int 5-Methyl dCN/A$50.00 USD$60.00 USD
3' PhosphorylationN/A$25.00 USD$30.00 USD
Int Spacer 18N/A$50.00 USD$60.00 USD

Machine-mixed bases are an option for Ultramer Oligonucleotides but hand-mixed bases are not available. Please inquire for other modifications.

4 nmole Ultramer oligo plates are loaded at 4 nmoles per well, and 20 nmole Ultramer oligo plates are loaded at 20 nmoles per well. Ultramer oligo plates are shipped either dried down or wet (frozen on dry ice) at 100 µM in 40 µL. Remainders in tubes or plates are not available on Ultramer oligo plates.

IDT has pioneered methods to synthesize and QC very long oligonucleotides, up to 200 bases in length, called Ultramer Oligonucleotides. Ultramer oligos can be used in a variety of molecular biology applications including, but not limited to:

  • Site-directed mutagenesis—used to efficiently and quickly generate large insertions, deletions or change stretches of sequence identity
  • In vitro transcription—templates for the synthesis of RNA
  • DNA-directed RNAi (ddRNAi)—hairpins are cloned into an expression vector, such as the GeneClip™ U1 Hairpin Cloning System (Promega)
  • DNA standards in qPCR reactions
  • Can be designed to span long regions of low complexity in a single oligonucleotide and still leave room for unique terminal sequences for assembly
  • Other molecular biology applications that require high purity oligonucleotides ranging in length from 45 to 200 bases

Ultramer Oligonucleotides are delivered deprotected and are purified through desalting, to remove small molecular impurities, or PAGE purification for extremely high purity needs. For even greater convenience, standard desalted Ultramer oligos are delivered normalized to the IDT guaranteed yield (4 nmoles). Standard, desalted Ultramer oligos are shipped dried down in 2–4 business days and PAGE-purified Ultramer oligos in 4–7 business days. 

As always at IDT, all oligos receive complimentary mass spectrometry QC. A custom, proprietary electrospray ionization (ESI) mass spectrometry method has been developed to provide accurate mass assessment up to 200 bases. All mass spectrometry QC traces are provided free of charge on the IDT website.

IDT employs proprietary DNA synthesis equipment which permits rapid, high quality synthesis of nucleic acids. This platform can be adapted to a lower throughput mode with an "extra rich" synthesis cycle. Our R&D team has developed synthesis chemistry and cycles which improve coupling efficiency above 99.5%, on average, through an entire 200 base synthesis reaction. Along with improvements in the synthesis cycle, we developed a unique solid support which is specifically optimized for synthesis of low-yield, high-quality oligos of up to 200 bases in length. The relationship between the percentage of full length product and the coupling efficiency is shown in Figure 1.

Figure 1. Oligonucleotide Yield is Determined by Coupling Efficiency.

Each cycle of chemical synthesis proceeds with a finite coupling efficiency. The first base is attached to the solid support which means a 20mer requires 19 coupling reactions and a 200mer requires 199 coupling reactions. Overall synthesis yield of full-length product is a function of both coupling efficiency and length according to the relationship:

Full-length product = (eff)(n–1)

where eff = coupling efficiency (for example, 99.5% = 0.995) and (n–1) is the number of coupling reactions needed to make an oligo of length n. The relationship between the percentage of full length product and the coupling efficiency is shown in Figure 1.

As demonstrated in Figure 1, the only way to synthesize a 200mer oligonucleotide with an appreciable yield of full length material (>30%) is to have a step-wise coupling efficiency >99.25%.

Typically, mass spectrometry is considered the gold standard for oligonucleotide synthesis QC. MALDI mass spectrometry is effective for products in the 10–50 base range. Above 50 bases, ESI (electrospray ionization) mass spectrometry can be employed and has an accuracy of better than 0.02% relative mass. Even with the sensitivity and accuracy of ESI-MS, performing QC on long oligonucleotides is complex. If a synthesis preparation is too impure, the various failure products will obscure the mass spectra, making it difficult to deconvolute and identify the desired species. Using our proprietary mass spectrometry methods, we can confidently synthesize and provide ESI-MS quality documentation for oligonucleotides up to 200 bases in length. ESI mass spectra for two Ultramer oligos are shown in Figure 2.

Figure 2 Figure 3

Figure 2. Mass Spectra Show High Purity of 185mer and 189mer Ultramer® Oligonucleotides.