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Characterization of Byproducts from Chemical Syntheses of Oligonucleotides Containing 1‑Methyladenine and 3‑Methylcytosine
- Source :
- ACS Omega, Vol 2, Iss 11, Pp 8205-8212 (2017), ACS Omega
- Publication Year :
- 2017
- Publisher :
- American Chemical Society, 2017.
-
Abstract
- Oligonucleotides serve as important tools for biological, chemical, and medical research. The preparation of oligonucleotides through automated solid-phase synthesis is well-established. However, identification of byproducts generated from DNA synthesis, especially from oligonucleotides containing site-specific modifications, is sometimes challenging. Typical high-performance liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoresis methods alone are not sufficient for characterizing unexpected byproducts, especially for those having identical or very similar molecular weight (MW) to the products. We used a rigorous quality control procedure to characterize byproducts generated during oligonucleotide syntheses: (1) purify oligonucleotides by different HPLC systems; (2) determine exact MW by high-resolution MS; (3) locate modification position by MS/MS or exonuclease digestion with matrix-assisted laser desorption ionization-time of flight analysis; and (4) conduct, where applicable, enzymatic assays. We applied these steps to characterize byproducts in the syntheses of oligonucleotides containing biologically important methyl DNA adducts 1-methyladenine (m1A) and 3-methylcytosine (m3C). In m1A synthesis, we differentiated a regioisomeric byproduct 6-methyladenine, which possesses a MW identical to uncharged m1A. As for m3C, we identified a deamination byproduct 3-methyluracil, which is only 1 Da greater than uncharged m3C in the ∼4900 Da context. The detection of these byproducts would be very challenging if the abovementioned procedure was not adopted.
- Subjects :
- 0301 basic medicine
Gel electrophoresis
Exonuclease
Chromatography
biology
Oligonucleotide
Chemistry
General Chemical Engineering
010401 analytical chemistry
General Chemistry
Mass spectrometry
01 natural sciences
High-performance liquid chromatography
Combinatorial chemistry
Article
0104 chemical sciences
lcsh:Chemistry
03 medical and health sciences
030104 developmental biology
lcsh:QD1-999
Desorption
biology.protein
Subjects
Details
- Language :
- English
- ISSN :
- 24701343
- Volume :
- 2
- Issue :
- 11
- Database :
- OpenAIRE
- Journal :
- ACS Omega
- Accession number :
- edsair.doi.dedup.....e1ac3ca0fb5711255112b0de402eaca6