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Oligo Modifications List | Oligo Modifications Reference Category
Modification : 3'-dG (2'-5' linked)
Reference Catalog Number 26-6492
Category Antisense
Modification Code dG(2'-5')
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 329.21
Extinction Coeficient (ec) 11.5
Technical Info (pdf) PS26-6492.pdf
Catalog NoScalePrice
26-6492-0550 nmol$355.00
26-6492-02200 nmol$355.00
26-6492-011 umol$461.50
26-6492-032 umol$692.25
26-6492-1010 umol$3,692.00
26-6492-1515 umol$4,615.00

Discounts are available for 3'-dG (2'-5' linked)!
Modification* Discount Price Structure
1 site/order List price
2 sites/order 10% discount
3 sites/order 20% discount
4 sites/order 30% discount
5-9 sites/order 50% discount
10+ sites/order 60% discount
*Exceptions apply

Related Modifications
3'-rG (2'-5' linked)
3'-dT (2'-5' linked)
3'-rC (2'-5' linked)
3'-rU (2'-5' linked)
3'-dA (2'-5' linked)
3'-dC (2'-5' linked)
3'-rA (2'-5' linked)

3'-deoxyguanosine (3’-dG)–(2'-5' linked) is deoxy at the 3’-position of the ribose, instead of at the usual 2’-position (note: the 3’-deoxynucleotides of A, C, and T are also available from Gene Link). 3’-deoxynucleotide (2’,5’-linked) modifications are used to substitute 2’-5’ phosphodiester linkages for the usual 3’-5’ phosphodiester linkages at some or all positions of an oligo. Oligonucleotides containing all, or primarily, 2’,5’-phosphodiester linkages selectively bind to complementary single-stranded 3’,5’-RNA over comparable 3,5’-DNA (1,2). This property means that DNA oligos containing such linkages could be useful in either anti-sense applications or as ssRNA-specific probes.

Bhan et al. (2) studied the potential for 2’,5’-linked DNA oligos as anti-sense molecules. High selectivity for 3’,5’ RNA over 3’,5’ DNA was observed, presumably due to the 2’,5’-linkages destabilizing duplexes formed with 3’,5’ DNA more than those formed with 3’,5’-RNA (for 2’,5’ DNA:3’,5’ RNA duplexes, DeltaTm is only about – 0.5 degC per 2’,5’ linkage substitution). Phosphorothiolation (which confers nuclease resistance) of 2’-5’ linkages lowers the Tm of 2’,5’ DNA:3’,5’ RNA duplexes even less, ~ – 0.2 degC per phosphorothiolated 2,’5’-linkage substitution. (by contrast, phosphorothiolation of a 3’,5’ linkage lowers the Tm of 3’,5’ DNA:RNA duplexes by – 0.5 to – 2.0 degC). Thus, 2’,5’-linked DNA oligos show both high selectivity and good duplex stability for RNA target sequences. However, 2’,5’-linked DNA oligos, whether phosphorothiolated or not, do not support RNAse H activity when bound to complementary RNA. But, substitution of six or seven contiguous 3’,5’ phosphorothiolate linkages into a 2’,5’ phosphorothiolated oligo at an appropriate place (that is, making a 2’,5’/3’,5’ phosphorothiolated chimera restores the oligo’s ability to support RNAse H activity. Furthermore, 2’,5’-linked DNA oligos, whether phosphorothiolated or not, show little or no non-sequence specific binding to cellular proteins (by contrast, 3’,5’ DNA oligos show considerable levels of such binding.

In summary, this research suggests that 2’,5’/3’,5’ phosphorothiolated chimeric oligos, in which 6-7 of the linkages are 3’,5’ to ensure that it can support RNAse H activity, have considerable potential as anti-sense reagents, due to their high selectivity for complementary RNA targets, and minimal non-sequence specific binding to cellular proteins.

In 2004, Sinha and co-workers showed that 2’,5’-linked DNA has some capability to function as a template for polymerase-directed DNA synthesis of the complementary strand (3). The authors showed several polymerases, and HIV reverse transcriptase, can successfully use a string of 2-4 2’,5’-linked DNA nucleotides as a template to synthesize its complementary strand with high fidelity, and speculated that the polymerases were serving as a “template for the template”, i.e., compensating for structural deficiencies in the 2’,5’-linked DNA that, in non-enzymatic contexts, would preclude genetic information transfer for 2’,5’-linked DNA.

References
1. Giannaris, P.A.; Damha, M.J. Oligoribonucleotides containing 2’,5’-phosphodiester linkages exhibit binding selectivity for 3’,5’-RNA over 3’,5’-ssDNA. Nucleic Acids Res (1993), 21: 4742-4749.
2. Bhan, P.; Bhan, A.; Hong, M.K.; Hartwell, J.G.; Saunders, J.M.; Hoke, G.D. 2’,5’-linked oligo-3’-deoxyribonucleoside phosphorothioate chimeras: thermal stability and antisense inhibition of gene expression. Nucleic Acids Res. (1997), 25: 40-41.
3. Sinha, S.; Kim, P.H.; Switzer, C. 2,5-Linked DNA Is a Template for Polymerase-Directed DNA Synthesis. J. Am. Chem. Soc. (2004), 126: 3310-3317.
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