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.
Coupling: Standard coupling time. Add a maximum of 2 times when using I2 oxidation or use 0.5M CSO in anhydrous acetonitrile and 3 min. oxidation time. (See Glen Report-Vol.9, No.1, 1996,page 8.)
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Specifications
Diluent
Anhydrous Acetonitrile
Storage
Refrigerated storage, maximum of 2-8°C, dry
Stability
3-5 days
Dilution/Coupling Data
The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.
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:
TBHP, anhydrous, 5-6M solution in decane (Aldrich 41,666-5)
Methylene chloride
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.
