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Duplex Stabilizing Bases

Incorporation of duplex stabilizing bases in a primers and/or probes for enhancing high affinity toward their target sequences with strong selectivity and sensitivity is critical in many molecular diagnostic and therapeutic systems. For antisense and siRNA knockdown experiment, incorporation of duplex stabilizing bases maybe needed to counteract the destabilizing effect of phoshorothioate linkage modification which often used to enhance nuclease resistance. In SNP detection experiment, binding affinity for its target can often be modulated by using duplex-stabilizing bases into SNP detection probe to improve mis-match discrimination. Example of using bridged mucleic acid, BNA base has shown to improve duplex stability by changing the melting temperature (Tm) of the duplex formed between the modified oligo and its target over that formed by the unmodified oligo. Depending on the modification, Tm can be increased over a range of 2oC to 4oC per base substitution. In addition, increasing the duplex stability using BNA can can augment the ability of an oligonucleotide to supress gene expression by forming stable DNA-RNA duplex and block translation via steric hindrance.

Bio-Synthesis degenerate site modification can be incorporated at any position of an oligonucleotide . Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

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Product Modification Code 5 Prime Internal 3 Prime Links
Bridged Nucleic Acids +A,+C,+G, +T Y Y Y Details
ZNA Spermine Z N N Y Details
2,6-Diaminopurine-2'-deoxyriboside DAPdR Y Y Y Details
2,6-Diaminopurine-2'-O-methylriboside DAPOMeR Y Y Y Details
2,6-Diaminopurine-riboside DAPR Y Y Y Details
5-Methyl-2'-deoxycytidine 5-Me-dC Y Y Y Details
5-Methylcytidine 5-Methyl-C Y Y Y Details
5-Methyl-2'-O-Methylcytidine 5-Methyl-2'-O-Methyl-C Y Y Y Details
5-Methyl-2'-deoxyisocytidine 5-Methyl-iC Y Y Y Details
2'-Deoxyisoguanosine iG Y Y Y Details
5-Propynyl-2'-deoxycytidine pdC Y Y Y Details
5-Propynyl-2'-deoxyuridine pdU Y Y Y Details
7-Deaza-8-aza-2'-deoxyadenosine 7-Deaza-8-aza-dA Y Y Y Details
N6-Methyl-deoxyadenosine N6-Me-dA Y Y Y Details
Aminoethyl-Phenoxazine-deoxycytosine AP-dC Y Y Y Details
5-Carboxy dC 5-carboxy-dC Y Y Y Details
2-Thio-dT 2-Thio-dT Y Y Y Details
2-Amino-deoxyadenosine dA 2-Amino dA Y Y Y Details
2’-O-Methyl uridine U mU Y Y Y Details
2’-O-Methyl guanosine G mG Y Y Y Details
2’-O-Methyl cytosine C mC Y Y Y Details
2’-O-Methyl adenosine A mA Y Y Y Details
2’-Fluoro-deoxyuridine (2’-F-U) 2-F-U Y Y Y Details
2’-Fluoro-deoxyguanosine (2’-F-G) 2-F-G Y Y Y Details
2’-Fluoro-deoxyacytosine (2’-F-C) 2-F-C Y Y Y Details
2’-Fluoro-deoxyadenosine (2’-F-A) 2-F-A Y Y Y Details
2’-F-A-ANA [FANA-A] Y Y Y Details
2’-F-Ac-A-ANA [FANA-Ac-A] Y Y Y Details
2’-F-G-ANA [FANA-G] Y Y Y Details
2’-F-U-ANA [FANA-U] Y Y Y Details
2’-F-5-Me-U-ANA [FANA-T] Y Y Y Details
5-Trimethoxystilbne Cap 5TMSC Y N N Details
5'-Pyrene Cap 5PYRC Y N N Details
3'-Uaq Cap 3UAQC N N Y Details
1,2-Dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate tripeptide CDPI3 Y N Y Details

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