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Bio-Synthesis offers hundreds of modified bases to be incorporated during oligonucleotide synthesis. These minor modified bases are often use to increase duplex stability and, therefore, melting temperature can be raised using the modified bases to improve in specificity and sensitivity for application where detection of small or highly similar DNA or RNA targets. The design of primers are often complicated by the degeneracy of the genetic code. Incorporation of mixed base addition (N), the use of 2'-deoxyInosine or '-deoxyNebularine, which exhibit low, but unequal, hydrogen bonding to the other four bases or the use of universal base offer solution for pulling out one part of a gene sequence in the related organisms. Minor modified bases have been used in biology and cancer research where the epigenetic control that define when and where which protein and gene products are expressed. Incorporation of minor modified bases in an oligonucleotide offer special utility in PCR and sequencing reaction. They are also useful products for the investigation on the effect and the activity of of an oligonucleotide when key structural elements are changed.

Minor base modifications are divided into following categories:

  • 2'-Deoxyribonucleoside Pyrimidines and Analogs
  • 2'-Deoxyribonucleoside Purine and Analogs
  • Ribonucleoside Analogs
  • 2'-Deoxyribonucleoside Purine and Analogs
  • Ribonucleoside Analogs
  • 2' O-Methyl Ribonucleoside Analogs
  • Sugar Modified Analogs
  • Wobble and Universal Bases

Contact Bio-Synthesis for Modified Base Oligonucleotide Synthesis Services.

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

Ordering & Contact Information

  • Please contact us for additional information or send an email to info@biosyn.com.
  • You may also request an online quote.
  • To contact us by phone, please call 1-972-420-8505 or Fax at 1-972-420-0442
  • Orders may be placed using a purchase order (PO) or by credit card through our secure online ordering system.
  • When using a credit card ( creditcard ) it will be billed under "Bio-Synthesis, Inc."