Several products may be used to investigate the effect on the activity of an oligonucleotide when key structural elements are changed. The 7-deaza purine monomers lack groups critical for hydrogen bonding. 7-Deaza-8-aza-A and 7-deaza-8-aza-G (PPG) monomers are isomers of A and G and have similar electron density. Their presence in oligos is slightly stabilizing relative to A and G. Unlike G, PPG does not lead to aggregation and G-rich oligos can be easily prepared and isolated. 5'-Fluorescein oligos with PPG at the 5'-terminus are much less quenched than the equivalent G oligos. As a purine analogue of Thymidine, 7-deaza-2'-deoxyXanthosine (7-deaza-dX) promises to have interesting effects on DNA structure of triplexes. 7-Deaza-dX also forms a non-standard base pair with a 2,4-diaminopyrimidine nucleoside analogue. Standard nucleobases have an unshared pair of electrons that project into the minor groove of duplex DNA. Enzymes that interact with DNA, polymerases, reverse transcriptases, restriction enzymes, etc., may use a hydrogen bond donating group to contact the hydrogen bond acceptor in the minor groove. 3-Deaza-2'-deoxyadenosine is very interesting in that it maintains the ability for regular Watson-Crick hydrogen bonding to T but is lacking the electron pair at the 3-position normally provided by N3.
REFERENCE(S)| 1 I.V. Kutyavin, et al., Nucleic Acids Res., 2002, 30, 4952-4959.
|Storage||Refrigerated storage, maximum of 2-8°C, dry|
The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.
|Catalog #||Pack Size||Grams/Pack||0.1M Dil. (mL)||Approximate Number of Additions|
|Catalog #||Pack Size||Grams/Pack||Dilution (mL)||Approximate Number of Additions|
Synthesis and Hybridizing Property of Oligonucleotides Including 2′-C,4′-C-Ethyleneoxy-Bridged 2′-Deoxyadenosine with an Exocyclic Methylene Unit Osawa, T., Onishi, Y., Wakita, S., Ito, Y., & Hari, Y.
DNA photo-cross-linking using a pyranocarbazole-modified oligodeoxynucleotide with a D-threoninol linker Fujimoto, K., Yamaguchi, T., Inatsugi, T., Takamura, M., Ishimaru, I., Koto, A., & Nakamura, S.
Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry Pradeep S. Pallan, Terry P. Lybrand, Eriks Rozners, Mikhail Abramov, Guy Schepers, Elena Eremeeva, Piet Herdewijn, and Martin Egli
In situations where you want to avoid the use of iodine containing oxidizing solutions, such as when using 7-deaza-dG, or when you want to use a non aqueous oxidizing solution t-butyl hydroperoxide (TBHP) has been shown to work both for DNA (1) and RNA (2). Reagents:
For DNA small scale: 1.1 M TBHP in Methylene Chloride, 0.8 min oxidation (1)For large scale RNA synthesis: 37ml TBHP solution + 63ml Methylene Chloride (approx. 2M), 6 min oxidation (2) Mix reagents fresh prior to use, oxidizing solution only stable for a few days on synthesizer.||REFERENCE(S):1. Hayakawa, Y., et al., JACS, 1990, 112, 1691., 2. Sproat, B., et al., Nucleosides & Nucleotides, 1995, 14, 255.