mRNA therapeutics · epigenomics · IVT-mRNA vaccine design · DNA repair assays
Nucleobase Modifications
Introduce epigenetic marks, damage site mimics, or IVT mRNA-optimized bases — essential for mRNA therapeutics, epigenetics research, and enzyme substrate studies.
| Category | Sub-category | Name (full) | Code | Applies to | Position | Function & mechanism (EN — for website copy) | Typical applications |
| Nucleobase Modifications | Methylation marks | 5-Methylcytosine (m5C / m5dC) | m5C / m5dC | DNA / RNA | Any C position | Epigenetic modification adding a methyl group to cytosine C5. Mimics natural CpG methylation. Used in studies of DNA methylation, epigenetic regulation, and RNA modifications. | Epigenetics research, methylated CpG probe controls, bisulfite sequencing standards |
| Nucleobase Modifications | Methylation marks | 5-Hydroxymethylcytosine (5hmdC) | 5hmdC | DNA | Any C position | Oxidized form of 5-methylcytosine found in mammalian brain and other tissues. Marker of active DNA demethylation. | Epigenetics research, 5hmC mapping, TET enzyme activity studies |
| Nucleobase Modifications | Methylation marks | N6-Methyladenine (m6A / m6dA) | m6A / m6dA | DNA / RNA | Any A position | Most abundant internal mRNA modification. Regulates mRNA stability, translation, and splicing. m6dA occurs in DNA of lower organisms. Critical for epitranscriptomics research. | m6A mapping (MeRIP-seq standards), epitranscriptomics, mRNA vaccine design |
| Nucleobase Modifications | Methylation marks | N1-Methylpseudouridine (m1ψ) | m1ψ | RNA | U positions | Combination of N1-methylation and pseudouridylation. Maximally reduces innate immune activation (TLR7/8) while maintaining high translational efficiency. Used in Moderna/BioNTech mRNA vaccine platforms. | mRNA therapeutics, mRNA vaccines (COVID-19 platforms), immunogenicity minimization |
| Nucleobase Modifications | Pseudouridine & analogs | Pseudouridine (ψ) | ψ | RNA | Any U position | C5-glycosidic isomer of uridine (uridine with the base rotated). Reduces TLR-mediated immune activation, increases RNA stability, and enhances translational efficiency in mRNA therapeutics. | mRNA therapeutics, in vitro transcribed RNA, immune evasion |
| Nucleobase Modifications | Pseudouridine & analogs | 5-Methyluridine (m5U) | m5U | RNA | Any U position | Methyl group at U-C5. Reduces immune activation and increases nuclease stability. Used as alternative to ψ in mRNA formulations. | mRNA therapeutics, immune-reduced RNA, synthetic mRNA |
| Nucleobase Modifications | Degenerate & universal bases | Deoxyinosine (dI) | dI | DNA / RNA | Any position | Universal base pairing A, C, T, and G with reduced discrimination. Used to reduce positional ambiguity in primers covering SNP positions, or to probe degenerate sequences. | Degenerate primer design, universal probe design, SNP-tolerant hybridization |
| Nucleobase Modifications | Degenerate & universal bases | Deoxyuridine (dU) | dU | DNA / RNA | T positions | RNA-like base in a DNA context. Cleaved by Uracil-DNA glycosylase (UNG). Used in UNG carryover prevention systems (AmpErase) to eliminate PCR amplicon contamination. | Carryover contamination prevention (UNG-based systems), hot-start PCR |
| Nucleobase Modifications | Degenerate & universal bases | 8-Oxo-deoxyguanosine (8-oxo-dG) | 8-oxo-dG | DNA / RNA | G positions | Major oxidative DNA damage product. Used as a damaged base standard in base-excision repair (BER) enzyme activity assays and oxidative stress studies. | DNA damage repair research, OGG1 enzyme assays, oxidative stress biomarkers |
| Nucleobase Modifications | Degenerate & universal bases | Inosine in RNA (rI) | rI | RNA | Any position | RNA-specific inosine. Present naturally in tRNA and mRNA editing. Used to study ADAR editing enzymes and as a wobble-position substitute in RNA sequences. | ADAR editing research, RNA modification studies, wobble position design |
| Nucleobase Modifications | IVT mRNA specific | N1-Methyladenine (m1A) | m1A | RNA | A positions | N1-methylation of adenosine. Occurs naturally in tRNA. Blocks Watson-Crick face for base pairing. Studied in context of RNA modification mapping. | Epitranscriptomics, RNA modification research, m1A antibody control |
| Nucleobase Modifications | IVT mRNA specific | EVP modified bases (EVP-mA/C/G/U) | EVP series | RNA | Any position | Engineered Vision Pharma (EVP) nucleotide analogs designed for enhanced translational output and reduced immunogenicity in synthetic mRNA. | Optimized mRNA therapeutics, translational efficiency enhancement |
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