Ultramer® DNA Oligonucleotides

Custom DNA oligos up to 200 bases

IDT has optimized proprietary synthesis methods to deliver high quality, long DNA oligos up to 200 bases. Known as Ultramer® DNA Oligonucleotides, these single-and double-stranded custom DNA oligos are available in tubes or plates, and are suitable for demanding applications such as cloning, ddRNAi, and gene construction.

Features

  • 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 DNA Oligos ship in 2–4 business days
  • PAGE-purified Ultramer DNA Oligos ship in 4–7 business days

Ultramer DNA 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.

Ultramer DNA Oligos in tubes

ProductPricingLength
4 nmole Ultramer®; DNA Oligo$1.25 SGD / Base45 - 200 BasesOrder
20 nmole Ultramer® DNA Oligo$2.40 SGD / Base45 - 200 BasesOrder
PAGE Ultramer®; DNA Oligo$1.25 SGD / Base60 - 200 BasesOrder

Ultramer DNA Oligos in plates

96-well plates require a minimum order of 24 oligos; 384-well plates require a minimum order of 96 oligos.
Sub-nanomole plates require a minimum order of 288 oligos.

ProductPricingLength96 Well384 Well
4 nmole Ultramer®; DNA Plate Oligo$0.65 SGD / Base45 - 200 BasesOrderOrder
20 nmole Ultramer® DNA Plate Oligo$1.30 SGD / Base45 - 200 BasesOrderOrder
ProductPricingLength96 Well384 Well
200 picomole Ultramer® DNA Plate Oligo$0.25 SGD / Base45 - 200 BasesOrderOrder

Ultramer DNA Duplexes in plates

96-well plates require a minimum order of 24 oligos; 384-well plates require a minimum order of 96 oligos.

ProductPricingLength96 Well384 Well
4 nmol Ultramer® Duplex Plate Oligo$0.65 SGD / Base45 - 200 BasesOrderInquire
20 nmol Ultramer® Duplex Plate Oligo$1.30 SGD / Base45 - 200 BasesOrderInquire

Ultramer oligonucleotide modifications

Delivered in tubes

Description4 nmole Ultramer®; DNA Oligo20 nmole Ultramer® DNA OligoPAGE Ultramer®; DNA Oligo
5' Phosphorylation$30.00 SGD$38.00 SGD$38.00 SGD
5' Biotin$68.00 SGD$83.00 SGD$67.00 SGD
5' Amino Modifier C6$32.00 SGD$48.00 SGDN/A
5' Amino Modifier C12$83.00 SGD$105.00 SGDN/A
5' deoxyInosine$15.00 SGD$18.00 SGD$18.00 SGD
5' deoxyUridine$15.00 SGD$18.00 SGD$18.00 SGD
Int deoxyInosine$15.00 SGD$18.00 SGD$18.00 SGD
Int deoxyUridine$15.00 SGD$18.00 SGD$18.00 SGD
Phosphorothioate Bond$5.50 SGD$5.50 SGD$5.50 SGD
2' O-Methyl RNA bases$14.00 SGD$23.00 SGD$23.00 SGD
3' Ribo A$45.00 SGD$60.00 SGD$60.00 SGD
3' Ribo C$45.00 SGD$60.00 SGD$60.00 SGD
3' Ribo G$45.00 SGD$60.00 SGD$60.00 SGD
3' Ribo U$45.00 SGD$60.00 SGD$60.00 SGD
3' Amino Modifier$42.00 SGD$53.00 SGDN/A
5' 5-Methyl dC$75.00 SGD$90.00 SGD$90.00 SGD
Int 5-Methyl dC$75.00 SGD$90.00 SGD$90.00 SGD
3' Phosphorylation$31.00 SGD$45.00 SGD$45.00 SGD
Int Spacer 18$75.00 SGD$90.00 SGD$90.00 SGD
3' C3 Spacer$68.00 SGD$83.00 SGD$83.00 SGD

Delivered in plates

Description200 picomole Ultramer® DNA Plate Oligo4 nmole Ultramer®; DNA Plate Oligo20 nmole Ultramer® DNA Plate Oligo
5' Phosphorylation$15.00 SGD$15.00 SGD$19.00 SGD
5' Biotin$30.00 SGD$30.00 SGD$38.00 SGD
5' Amino Modifier C6$18.00 SGD$18.00 SGD$27.00 SGD
5' Amino Modifier C12$42.00 SGD$42.00 SGD$53.00 SGD
5' deoxyInosine$6.00 SGD$6.00 SGD$7.50 SGD
5' deoxyUridine$6.00 SGD$6.00 SGD$7.50 SGD
Int deoxyInosine$6.00 SGD$6.00 SGD$7.50 SGD
Int deoxyUridine$6.00 SGD$6.00 SGD$7.50 SGD
Phosphorothioate Bond$5.50 SGD$5.50 SGD$5.50 SGD
2' O-Methyl RNA bases$14.00 SGD$14.00 SGD$23.00 SGD
3' Ribo AN/A$45.00 SGD$60.00 SGD
3' Ribo CN/A$45.00 SGD$60.00 SGD
3' Ribo GN/A$45.00 SGD$60.00 SGD
3' Ribo UN/A$45.00 SGD$60.00 SGD
3' Amino ModifierN/A$42.00 SGD$53.00 SGD
5' 5-Methyl dCN/A$75.00 SGD$90.00 SGD
Int 5-Methyl dCN/A$75.00 SGD$90.00 SGD
3' PhosphorylationN/A$31.00 SGD$45.00 SGD
Int Spacer 18N/A$75.00 SGD$90.00 SGD

Ultramer DNA Oligos are compatible with machine-mixed bases, but hand-mixed bases are not available. Please inquire for other modifications.

4 nmol plates are loaded at 4 nmol per well, and 20 nmol plates are loaded at 20 nmol per well. Plates can be shipped dried down, or wet (frozen on dry ice) at 100 µM in 40 µL. Remainders in tubes or plates are not available.

IDT has pioneered methods to synthesize and QC long DNA oligos up to 200 bases in length, called Ultramer® DNA Oligonucleotides. Ultramer DNA 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 DNA Oligos 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 DNA Oligos are formulated to IDT guaranteed yields (4 nmol, 20 nmol, 200 pmol).

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.