Determination of optical density (OD) of oligodeoxynucleotide from HPLC peak area

Chillar, Komal; Yin, Yipeng; Eriyagama, Adikari M. D. N.; Fang, Shiyue

doi:10.7717/peerj-achem.20

Cited by 4 publications

(4 citation statements)

References 5 publications

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“…OD 260 of all ODNs were determined using a reported method. 15 HPLC profiles, MS images, CE profiles and OD 260 values of all ODNs are in Fig. 3 and 4 or ESI †…”

Section: Methodsmentioning

confidence: 99%

Oligonucleotide synthesis under mild deprotection conditions

et al. 2023

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“…OD 260 of all ODNs were determined using a reported method. 15 HPLC profiles, MS images, CE profiles and OD 260 values of all ODNs are in Fig. 3 and 4 or ESI †…”

Section: Methodsmentioning

confidence: 99%

Oligonucleotide synthesis under mild deprotection conditions

et al. 2023

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“…The fractions of ODN were collected and concentrated to dryness. ODNs were quantified using a reported method, 19 and analyzed using MALDI-TOF MS and capillary electrophoresis.…”

Section: Methodsmentioning

confidence: 99%

PEGylated Dmoc phosphoramidites for sensitive oligodeoxynucleotide synthesis

Chillar,

Yin,

Apostle

et al. 2023

Org. Biomol. Chem.

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“…The HPLC profile of purified Tr-off 7 is shown in Figure 3. The OD 260 for the 0.52 μmol synthesis is calculated to be 0.24 according to the intensity of the HPLC peak (Chillar et al, 2022).…”

Section: Evaporate Volatiles In a Centrifuge Vacuum Concentratormentioning

confidence: 99%

Oligodeoxynucleotide Synthesis Under Non‐Nucleophilic Deprotection Conditions

Fang,

Chillar,

Yin

et al. 2024

Current Protocols

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This protocol describes a method for the incorporation of sensitive functional groups into oligodeoxynucleotides (ODNs). The nucleophile‐sensitive epigenetic N4‐acetyldeoxycytosine (4acC) DNA modification is used as an example, but other sensitive groups can also be incorporated, e.g., alkyl halide, α‐haloamide, alkyl ester, aryl ester, thioester, and chloropurine groups, all of which are unstable under the basic and nucleophilic deprotection and cleavage conditions used in standard ODN synthesis methods. The method uses a 1,3‐dithian‐2‐yl‐methoxycarbonyl (Dmoc) group that carries a methyl group at the carbon of the methoxy moiety (meDmoc) for the protection of exo‐amines of nucleobases. The growing ODN is anchored to a solid support via a Dmoc linker. With these protecting and linking strategies, ODN deprotection and cleavage are achieved without using any strong bases and nucleophiles. Instead, they can be carried out under nearly neutral non‐nucleophilic oxidative conditions. To increase the length of ODNs that can be synthesized using the meDmoc method, the protocol also describes the synthesis of a PEGylated Dmoc (pDmoc) phosphoramidite. With some of the nucleotides being incorporated with pDmoc‐CE phosphoramidite, the growing ODN on the solid support carries PEG moieties and becomes more soluble, thus enabling longer ODN synthesis. The ODN synthesis method described in this protocol is expected to make many sensitive ODNs that are difficult to synthesize accessible to researchers in multiple areas, such as epigenetics, nanopore sequencing, nucleic acid‐protein interactions, antisense drug development, DNA alkylation carcinogenesis, and DNA nanotechnology. © 2024 Wiley Periodicals LLC.Basic Protocol: Sensitive ODN synthesisSupport Protocol 1: Synthesis of meDmoc‐CE phosphoramiditesSupport Protocol 2: Synthesis of a pDmoc‐CE phosphoramidite

show abstract

Determination of optical density (OD) of oligodeoxynucleotide from HPLC peak area

Cited by 4 publications

References 5 publications

Oligonucleotide synthesis under mild deprotection conditions

Oligonucleotide synthesis under mild deprotection conditions

PEGylated Dmoc phosphoramidites for sensitive oligodeoxynucleotide synthesis

Oligodeoxynucleotide Synthesis Under Non‐Nucleophilic Deprotection Conditions

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