Have named quenched autoligation (QUAL) probes.3 QUAL probes consist of two oligonucleotides, the first containing a nucleophilic group at the 3′-terminus, while the second has an electrophilic group at the 5′-terminus. When the probe pair finds the target, the oligos line up with the 3′-terminus of the first directly adjacent to the 5′-terminus of the second. A Kool autoligation reaction then takes place to combine the two oligos into a single probe. As usual, the 3′ nucleophilic group is the 3-thiophosphate easily prepared using 3’phosphate CPG with a sulfurizing step in the first cycle. In this case, the electrophilic group is a 5′-dabsyl group, which is an excellent leaving group as well as a fine quencher of fluorescence. The second oligo, therefore, contains a fluorophore which is quenched by the dabsyl group. A popular choice for fluorophore is fluorescein-dT but it is easy to imagine that a variety of fluorophores could be attached to any of the commercially available amino-modified nucleoside phosphoramidites. The process is illustrated in Figure 1. The efficacy of this procedure has recently been illustrated in intact cells. Using fluorescence microscopy or flow cytometry, QUAL probes were able to distinguish single nucleotide differences in the 16S rRNA 10

FIGURE 2: STRUCTURE OF 5′-DABSYL-DT

(1) 5′-Dabsyl-dT

i

sequences of three closely related bacteria. Even a single mismatch was revealed by a significant decrease in fluorescence signal.4 By combining QUAL with FRET, Abe and Kool were able to substantially reduce the background signal arising from the release of the dabsyl group.53-84-9 Molecular Weight In this way, they were able to detect and quantify three different messenger RNAs, as well as 28S ribosomal RNA, by flow cytometry.5 Glen Research is happy to offer 5’Dabsyl-dT CE Phosphoramidite (1) to allow ORDERING
SELENIUM DERIVATIzATION OF NUCLEIC ACIDS FOR X-RAY CRYSTAL STRUCTURE DETERMINATION
Zhen Huang, Ph.D. Department of Chemistry Georgia State University Atlanta, Georgia 30303 Determination of the three-dimensional structures of RNA molecules, RNA-protein and DNA-protein complexes with high resolution is invaluable for gaining understanding of biological systems at the molecular level.129298-91-5 IUPAC Name X-ray crystallography is the most direct and powerful tool for structure determination of these macromolecules.PMID:29999795 However, besides the difficulties related to crystallization, heavy atom derivatization for phase determination has been a longstanding problem in nucleic acid X-ray crystallography that has largely slowed down structural determination of new structures and folds. The conventional approaches for DNA and RNA derivatization, such as heavyatom soaking and co-crystallization, have proved to be much more difficult for nucleic acids than for proteins, probably because nucleic acids often lack specific binding sites for metal ions. In addition, the radiation stability and structure perturbation have reduced the usefulness of the halogen derivatization (such as Br and I). Recently, we have successfully demonstrated a novel derivatization strategy via selenium replacement of oxygen in nucleic acids.1-8 Unlike conventional halogen derivatization (Br or I), where halogens are primarily placed on the 5-position of deoxyuridine (a mimic of thymidine), selenium can be selectively introduced to a variety of positions via oxygen replacement (e.g., 2′-, 3′-, 5′-ribose oxygen, furan ring oxygen, non-bridging phosphate oxygen, or oxygen on nucleobases).1-8 Choice of pos.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