Bio-Synthesis offers a vast number of useful modified base analogs to be incorporated during oligonucleotide synthesis. In medicine, several of these base analogs are used as anticancer or antiviral agents. Modified bases such as bridged nucleic acid (BNA) can also be used to modulate Tm of short oligos, as it often serves to protect oligonucleotide from enzyme degradation. Modified bases such as 2′-Fluoro-Uridine, 5-Methyl-deoxyCytidine, 2,6-Diaminopurine or Iso-deoxyGuanosine can be used too in place of the standard T, C, A or G to avoid mismatch detection and repair for oligo-mediated allelic-replacement experiment.
Modified bases can be incorporated into RNA or DNA at multiple sites during synthesis. We recommend purification since some nucleosides are more difficult to incorporate to an oligonucleotide when multiple sites are required.
Effects of Oligonucleotide analogues
Base modification can change oligonucleotide mass and sometimes alter UV absorbance, molecular weight and melting temperature (TM).
Example of melting temperature (TM) can be changed when oligonucleotide are modified with phosphorothioate since it reduce TM significantly. In contrast, BNA nucleotides increase Tm from 2-4 oC. Unfortunately, nearest neighbor thermodynamic parameters have not been determined for a majority of base mimic analogs. Therefore, no accurate parameters and physical models exist that would allow us to calculate melting temperatures for many modified base oligonucleotides. Internal base modifications (e.g., biotin-dT), could collide and interfere with the duplex structure. Because the quantitative effects of interference are unknown, functional assay to optimize experiment is necessary.
Custom Modified Base Oligonucleotide Synthesis
Bio-synthesis offers numbers of modified bases that can be mixed with RNA or DNA synthesis. Purification is recommended for modified base oligo synthesis. 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.
Browse our selection of modified bases using the tabs below. When you ready to design and order your oligonucleotide, simply click on the order button. Alternatively, let us design the oligonucleotide for you.
2'-Deoxyribonucleoside Pyrimidines and Analogs
List of deoxyribonucleoside pyrimidine modified bases we offer are:
- 2'-Deoxypseudouridine
- 2'-Deoxyuridine
- 2-Thiothymidine
- 4-Thio-2'-deoxyuridine
- 4-Thiothymidine
- 5' Aminothymidine
- 5-(1-Pyrenylethynyl)-2'-deoxyuridine
- 5-(C2-EDTA)-2'-deoxyuridine
- 5-(Carboxy)vinyl-2'-deoxyuridine
- 5,6-Dihydro-2'-deoxyuridine
- 5-Bromo-2'-deoxycytidine
- 5-Bromo-2'-deoxyuridine
- 5-Carboxy-2'-deoxycytidine
- 5-Fluoro-2'-deoxyuridine
- 5-Formyl-2'-deoxycytidine
- 5-Hydroxy-2'-deoxycytidine
- 5-Hydroxy-2'-deoxyuridine
- 5-Hydroxymethyl-2'-deoxycytidine
- 5-Hydroxymethyl-2'-deoxyuridine
- 5-Iodo-2'-deoxycytidine
- 5-Iodo-2'-deoxyuridine
- 5-Methyl-2'-deoxycytidine
- 5-Methyl-2'-deoxyisocytidine
- 5-Propynyl-2'-deoxycytidine
- 5-Propynyl-2'-deoxyuridine
- 6-O-(TMP)-5-F-2'-deoxyuridine
- C4-(1,2,4-Triazol-1-yl)-2'-deoxyuridine
- C8-Alkyne-thymidine
- dT-Ferrocene
- N4-Ethyl-2'-deoxycytidine
- O4-Methylthymidine
- Pyrrolo-2'-deoxycytidine
- Thymidine Glyco
2'-Deoxyribonucleoside Purine Modified Bases
List of 2'-Deoxyribonucleoside Purine modified bases we offer are:
- 2,6-Diaminopurine-2'-deoxyriboside
- 2-Aminopurine-2'-deoxyriboside
- 6-Thio-2'-deoxyguanosine
- 7-Deaza-2'-deoxyadenosine
- 7-Deaza-2'-deoxyguanosine
- 7-Deaza-2'-deoxyxanthosine
- 7-Deaza-8-aza-2'-deoxyadenosine
- 8-5'(5'S)-Cyclo-2'-deoxyadenosine
- 8-Amino-2'-deoxyadenosine
- 8-Amino-2'-deoxyguanosine
- 8-Bromo-2'-deoxyadenosine
- 8-Bromo-2'-deoxyguanosine
- 8-Deuterated-2'-deoxyguanosine
- 8-Oxo-2'-deoxyadenosine
- 8-Oxo-2'-deoxyguanosine
- Etheno-2'-deoxyadenosine
- Formylindole
- N6-Methyl-2'-deoxyadenosine
- O6-Methyl-2'-deoxyguanosine
- OX6-Phenyl-2'deoxyinosine
Ribonucleoside Modified Bases
List of ribonucleoside modified bases we offer are:
- 2,6-Diaminopurine-riboside
- 2-Aminopurine-riboside
- 4-Thiouridine
- 5-Bromouridine
- 5-Iodouridine
- 5-Methylcytidine
- 5-Methyluridine Inosine
- Pseudouridine
- Puromycin
- Pyrrolocytidine
2'-O-Methyl Ribonucleoside Modified Bases
List of ribonucleoside modified bases we offer are:
- 2,6-Diaminopurine-2'-O-methylriboside,6-Diaminopurine-riboside
- 2-Aminopurine-2'-O-methylriboside
- 2'-O-Methylinosine
- 3-Deaza-5-Aza-2'-O-methylcytidine
- 5-Bromo-2'-O-methyluridine
- 5-Fluoro-2'-O-Methyluridine
- 5-Fluoro-4-O-TMP-2'-O-Methyluridine
- 5-Methyl-2'-O-Methylcytidine
- 5-Methyl-2'-O-Methylthymidine
Sugar Modified Bases
List of sugar modified bases we offer are :
- 2',3'-Dideoxyadenosine
- 2',3'-Dideoxycytidine
- 2',3'-Dideoxyguanosine
- 2',3'-Dideoxythymidine
- 3'-Deoxyadenosine
- 3'-Deoxycytidine
- 3'-Deoxyguanosine
- 3'-Deoxythymidine
- 5'-Iodothymidine
- 5'-O-Methylthymidine
- Azacytidine
- Bridged Nucleic Acid (BNA)
Wobble and Universal Bases
List of sugar modified bases we offer are:
- 2' Deoxynebularine
- 2'-Deoxyinosine
- 2'-Deoxyisoguanosine
- 3-Nitropyrrole-2'-deoxyribose
- 5-Nitroindole-2'-deoxyriboside
- K-2'-deoxyribose
- P-2'-deoxyribose
- Pyrrolidine
- Wobble Site