N the sequence length as well as sequence content. Longer oligonucleotides will be more hydrophilic, reducing the impact of hydrophobic labels on overall polarity. Also, the presence of other modifications can interfere as in the case of dual-labeled fluorescent probes, such as those used in Fluorescence Resonance Energy Transfer (FRET).3 If the hydrophobicity of the 3′-label is similar to or greater than that of DMT (Figures 1-2), the DMT-OFF failure oligonucleotide sequences will bind to the support and co-purify with the desired product. The
same effect applies to internally placed hydrophobic modifications. In summary, the relative RP-HPLC RT’s of 5′-labeled oligonucleotides appear to be reliable predictors of GlenPak compatibility, and this should be considered as a planning guide as one decides what purification methods to employ.67-68-5 SMILES As always, one may also consider using Glen-Pak purification in tandem with another purification method in order to achieve their ultimate desired purity.83602-39-5 custom synthesis
Product Review — Rhodamine Dyes
In our previous volume, 34.2, fluorescein dyes were discussed.1 Another popular family of fluorophores is the rhodamine dyes. They are bright dyes that are used in many of the same applications where fluorescein dyes are used including water tracing, paper/textile coloring, food additives (illegally) and biotechnology. The last of these is, of course, the most interesting for our customers. TAMRA is the most common of the rhodamine dyes, at least for oligonucleotide labeling. It is short for TetrA Methyl RhodAmine and consists of rhodamine and four methyl substitutions on the two exocyclic amines (Figure 1). Like most rhodamine dyes, the structure exists as predominantly an equilibrium between the open, zwitterionic fluorescent form (right) and the closed non-fluorescent lactone (left). The small molecule dye has excitation and emission wavelengths of 556 and 580 nm, respectively, and exhibits a pink color. It should be noted that the TAMRA excitation overlaps well with the emission of fluorescein. Although we typically refer to TAMRA as a fluorophore, it is very commonly used as a quencher for fluorescein and its substituted derivatives such as TET and Yakima Yellowin dual-labeled probes. Glen Research offers three options for TAMRA labeling. There are 3′-TAMRA CPG/PS supports to facilitate 3′-labeling. There is also a TAMRA-dT that can be placed anywhere in the oligonucleotide. Finally, there is an NHS ester that can be attached to any one of our many amino-modifiers via post-synthetic modification. This last approach serves two important purposes.PMID:31424732 1. Since there is no 5′-TAMRA phosphoramidite available, the NHS ester is the default choice for 5′-labeling. 2. Due to the incompatibility of TAMRA with standard ammonia-based deprotection methods, the NHS ester approach gives researchers additional deprotection options for more challenging to synthesize sequences.
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Glen Research also carries other derivatives of rhodamine (Figure 2). Just like our fluorescein family, these derivatives have substitutions on the aromatic rings that red-shift the spectral properties of the fluorophores (Table 1). ROX has additional alkyl rings derived from julolidine and is available as an NHS ester to facilitate post-synthetic conjugation. The core structure of ROX is also available in the form of a 5′-phosphoramidite and CPG as AquaPhluor593 (AP593). Further substitution and modification of AP593 gives rise to AquaPhluor639 (AP639). AP593 an.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com
