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Frequently asked questions for Oligo Synthesis and siRNA

• Oligonucleotide FAQ’s
• siRNA FAQ’s

Oligo Handling and Storage


Q1. How should I store my oligo?

Q2. How should I resuspend my oligo?

Q3. If oligos were left at room temperature for more than a week, would they still work?

Q4. Do I have to treat fluorescent dye modified oligos differently in storage and handling?


Quantity and Concentration


Q5. How does Bioneer quantify my oligo?

Q6. How do I calculate the oligo quantity from the measured OD value?

Q7. If the O.D. value of an 18 mer oligo containing 3dG, 4dC, 5dA and 6T is 0.7, how much oligo is there?

Q8. How do we calculate the molecular weight of an oligonucleotide?

Q9. How do I convert oligo quantity expressed in nmole into weight?

Q10. When I do not know the exact base composition, is there any method to quantify the synthesized oligo?

Q11. How do I measure Tm of the synthesized oligo?

Q12. Why are there differences in Tm value that Bioneer provided and mine?

Q13. What is the method for adjusting the oligonucleotide concentration?

Q14. Unit conversions


Synthesis and Order


Q15. How are oligonucleotides synthesized?

Q16. Standard oligo structure.

Q17. What are base limitations on each synthesis scale?

Q18. When I ordered the 50 nmole scale, I got less than 50nmoles. What happened?

Q19. Can you make the oligos having a high percentage of "G" residues?

Q20. Do you provide oligoribonucleotide (RNA) synthesis?

Q21. Does the oligo synthesized have phosphate group at 5’ or 3’ position?

Q22. What are the symbols denoting degenerate bases?


Purification


Q23. How do you purify the oligos synthesized?

Q24. How is long-mer oligo for microarray purified?

Q25. Oligo modifications.

Q26. Phosphorothioate oligo as an antisense ODN.