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The stability of the RNA-DNA duplex in terms of hybridization and half-life is crucial to successful gene inhibition. Synthetic oligonucletoides used in cell culture or in vivo experiments often face the chanllenge of degradation as well as chemical instability which often lead to fast degradation with a finite half life1. While unmodified DNA and RNA oligos are quickly digested in vitro and in vivo by multiple endo- and exonuceases2, vigorous research activity in the area of nucleic acid chemistry has been devoted in developing novel base analogs to block nuclease degradation, at same time, retain its molecular structure and base interaction. This crucial property is indispensable for gene silencing experiments - such as in antisense, RNAi and in ribozyme technology. To limit nuclease sensitivity and enhancing intracellular statbility, many different oligo modifications into native phosphodiester oligodeoxyribonucleotide and ribonucleotide polymers are available

Bio-Synthesis offers an extensive array of modifications to accomplish duplex stability and nuclease resistance to synthetic oligos. We have the ability to synthesize complex combinations of modifications and chimeric oligos. In addition to the synthesis of these modified oligos, we routinely assist customers in the design of the oligos that are particularly suited to their application. Common modification sites are:

  • Phosphodiester linkages : phoshorothioate, methylphosphonate, dithiol, 3'-3' end linkage for exonuclease resistance
  • Sugar substitutions : Bridged Nucleic Acids (BNA), 2'O-Methyl, 2'-Fluoro for endonucease resistance
  • Nucleic acid bases : 2 amino dA, 5-Methyl dC, propyne dC, propyne dU
  • Mirror-image L-nucleotide : L-DNA, L-RNA
  • Functional group addition 3' phosphorylation or addition of C3 spacer

Contact Bio-Synthesis for oligo modification to block nuclease degradation.

All oligonucleotide synthesized at Bio-Synthesis is quality check by using either MALDI-TOF mass spectrometry, analytical HPLC,or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform custom formulation and quality control tailored to meet your specific requirements.

Nuclease Resistant Modified Oligos Chemistry 5' Prime Internal 3' Prime
BNA Y Y Y
2'-O Methyl Adenosine A mA Y Y Y
2'-O Methyl Cytosine C mC Y Y Y
2'-O Methyl Guanosine G mG Y Y Y
2'-O Methyl Uridine U mU Y Y Y
2'-Fluoro deoxyadenosine (2'-F-A) 2-F-A Y Y Y
2'-Fluoro deoxycytosine (2'-F-C) 2-F-C Y Y Y
2'-Fluoro deoxyguanosine (2'-F-G) 2-F-G Y Y Y
2'-Fluoro deoxyuridine (2'-F-U) 2-F-U Y Y Y
propyne dC deoxycytosine pdC Y Y Y
propyne dU deoxyuridine pdU Y Y Y
L-DNA Y Y Y
L-RNA Y Y Y
Inverted dA (5'-5' or 3'-3' linkage) inv-dA Y Y Y
Inverted dA (5'-5' or 3'-3' linkage) inv-dC Y Y Y
Inverted dA (5'-5' or 3'-3' linkage) inv-dG Y Y Y
Inverted dT (5'-5' or 3'-3' linkage) inv-dT Y Y Y
Inverted rA (5'-5' or 3'-3' linkage) rev-rA Y Y Y
Inverted rC (5'-5' or 3'-3' linkage) rev-rC Y Y Y
Inverted rG (5'-5' or 3'-3' linkage) rev-rG Y Y Y
Inverted rU (5'-5' or 3'-3' linkage) rev-rU Y Y Y
Inverted 2',3' dideoxy dT (5' Inverted ddT) ddT-5' Y Y Y
Phosphorothioate (PS) Bonds * Y Y Y
Methylphosphonate MP Y Y Y
Phosphorylation P Y Y Y
C3 Spacer SPC3 Y Y Y

Quality Control: Analytical HPLC, Gel eletrophoresis, and  MALDI-TOF Mass Spectrometry

Delivery times: 5-7 Working days

Packaging:    Dried

Shipping conditions: Room temperature

Storage conditions: -20 oC to -70 oC

Oligonucleotides are stable in solution at 4 oC for up to 2 weeks. Properly reconstituted material stored at -20 oC should be stable for at least 6 months. Dried DNA (when kept at -20 oC) in a nuclease-free environment should be stable for years.

References :
  • Cazenave, C., Chevrier, M., Nguyen, T.T., Helene, C. Rate of degradation of [alpha]- and [beta]-oligodeoxynucleotides in Xenopus oocytes. Implications for anti-messenger strategies. Nucleic Acids Res. (1987), 15: 10507-10521.
  • Fisher TL, Terhorst T, et al. (1993) Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into mammalian cells. Nucleic Acids Res, 21:3857−3865.

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."