Internal and 5' Positions
These modifications can also be inserted at the 3' end of an oligonucleotide using special procedures. Please inquire.
dInosine, dUridine and Universal Bases
Degeneracy of the genetic code often complicates the design of primers and probes. Degenerated oligonucleotides can be synthesized using mixed positions, but it is only useful for a small number of sites. Deoxyinosine exhibits low but unequal hydrogen bonding to the other four bases. Universal base (5-nitroindole) does not discriminate between the four bases. The pyrimidine derivative P base pairs with A or G and the purine derivative K base pairs with C or T.
Pricing is per position in addition to basecharge.
Incorporation of 5-Methyl-deoxyCytosine, N4-Ethyl-deoxyCytosine or 2-Amino-eoxy Adenosine(2.6-diaminopurine) at single or multiple positions within or as 5'-nucleotide of an oligonucleotide will result in some duplex effects. Replacement of dC with 5-Me-dC increases Tm with 1.3°C and dA with 2-amino-dA increases Tm with 3°C. Replacement of dC with N4-Et-dC decreases Tm with 2°C.
|Tm Effect||+1.3 °C||+3 °C||-2 °C|
Methyl, Halogen and Sulfur
Methylated, halogenated and sulfur-modified nucleotides can be incorporated at single or multiple positions of an oligonucleotide.
Oligonucleotides with methylated nucleotides can be useful in studies of mutagenic effects.
Halogenated oligonucleotides are often used for crystallography and cross-linking studies of protein-DNA complexes. Halogenated nucleotides can be incorporated at single or multiple positions of an oligonucleotide.
Sulfur-modified oligonucleotides are useful for photocrosslinking and photo labeling experiments.
Amino Groups and Carboxy-dT
Primary amines or carboxy-dT can be incorporated at single or multiple positions within or at 5' end of an oligonucleotide.
- Amino TEG mdC
Internal Amino-C4 and -CX are incorporated on a propanediol linker in between the deoxyribophosphates in the oligonucleotide backbone. The Amino-CX is an amino group on a flexible 8 atomic linker on cyclohexane.
Biotin can be incorporated at single or multiple positions within or at 5'end of an oligonucleotide. Internal Biotin-C4 and -CXS are incorporated on a propanediol and Biotin-TEG (triethylene glycol) on an ethanediol linker in between the deoxyribosephosphates in the oligonucleotide backbone. Biotin-CXS is an analog to Biotin-C4 in which case the butane linker is substituted with cyclohexane.
Fluorescent Dyes and Quenchers
Incorporation of fluorescent dyes or quenchers at single or multiple positions within an oligonucleotide is possible on linkers in between the deoxyribophosphates in the oligonucleotide backbone or on dT.
- Quasar® 570 (Cy3 analog)
- Quasar 670 (Cy5 analog)
- CAL Fluor® Red 610 (Cy3.5 analog)
- Quasar 705 (Cy5.5 analog)
See fluorescent dyes for emission data
HEG spacer (hexaethylene glycol) is an 18 atom spacer and TEG spacer (triethylene glycol) is a 9 atom spacer of mixed polarity. dSpacer (deoxyribophosphate) is an abasic position. PC spacer is a photo-cleavable spacer.
- PC spacer
Oligonucleotide trees with combined structures of either symmetric or asymmetric (Asymmetric Doubler) character can be created using symmetric (Symmetric Doubler, Trebler) or asymmetric (Asymmetric Doubler) branching modifiers.
- Asymmetric Doubler
- Symmetric Doubler
As the list is continuously increasing, please contact us for updates, further information or specific inquiries and demands.