5-Hydroxymethyl-2'-deoxyuridine, 5-hmdU
5-Hydroxymethyl-2'-Deoxyuridine (5-hmdU) is a modified pyrimidine nucleoside in which the methyl group normally present in thymidine is replaced by a hydroxymethyl (-CH₂OH) group. This naturally occurring DNA modification is found in the genomes of several bacteriophages, including bacteriophage T4, where it contributes to protection against host restriction enzymes and influences DNA-protein interactions.
Because the hydroxymethyl substituent alters the chemical and biological properties of DNA without significantly disrupting Watson-Crick base pairing, 5-hmdU has become an important research tool for investigating DNA recognition, epigenetic mechanisms, DNA repair, and enzyme specificity. The modification can also serve as a precursor for additional chemical derivatization or enzymatic modification, providing flexibility for advanced molecular biology applications.
Oligonucleotides containing 5-hmdU are frequently used to examine how modified pyrimidines influence DNA duplex stability, polymerase activity, nuclease resistance, transcription factor binding, and interactions with DNA-binding proteins. They are also valuable for studying naturally modified bacteriophage DNA and for engineering synthetic nucleic acids with unique biological properties.
Typical applications include:
- DNA epigenetics research
- DNA modification studies
- Bacteriophage DNA research
- DNA-protein interaction studies
- DNA polymerase studies
- DNA repair mechanisms
- Restriction enzyme recognition
- Synthetic biology
- DNA nanotechnology
- Molecular diagnostics
Bio-Synthesis offers custom DNA oligonucleotides containing 5-Hydroxymethyl-2'-Deoxyuridine synthesized using optimized solid-phase phosphoramidite chemistry. The modification can be incorporated at one or multiple defined positions and combined with numerous additional chemistries, including fluorophores, quenchers, biotin, amino modifiers, thiol modifiers, click chemistry handles, PEG linkers, and other custom conjugates.
Each modified oligonucleotide is manufactured under stringent quality standards and is available with optional desalting, HPLC purification, or PAGE purification, together with analytical characterization by LC-MS, MALDI-TOF, capillary electrophoresis, and additional quality control testing to ensure product identity and purity.
| Property |
Typical Value |
| Modification |
5-Hydroxymethyl-2'-Deoxyuridine (5-hmdU) |
| Base Family |
Modified pyrimidine nucleobase |
| Parent Base |
Thymidine / Deoxyuridine analog |
| Chemical Modification |
5-Hydroxymethyl substitution |
| Sugar |
2'-Deoxyribose |
| Base Pairing |
Pairs with adenine (A) |
| Compatible Oligos |
DNA oligonucleotides |
| Typical Applications |
Epigenetics, bacteriophage DNA, DNA repair, synthetic biology, DNA-protein interaction studies |
Product Information
5-Hydroxymethyl-2'-deoxyuridine, 5-hmdU
-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years.
References/Citations:
- Warren RA. Modified bases in bacteriophage DNAs. Annual Review of Microbiology. 1980;34:137-158. DOI: 10.1146/annurev.mi.34.100180.001033
- Blackburn GM, Gait MJ, Loakes D, Williams DM. Nucleic Acids in Chemistry and Biology. 3rd ed. Royal Society of Chemistry; 2006.
- Herdewijn P, ed. Modified Nucleosides in Biochemistry, Biotechnology and Medicine. Wiley-VCH; 2008.
- Kornberg A, Baker TA. DNA Replication. 2nd ed. University Science Books; 1992.
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