Development of drug resistance against chemotherapeutic reagents. One of the most studied repair mechanisms is probably the base excision DNA repair pathway. In this pathway, DNA glycosylases recognize the damaged bases and catalyze their excision through hydrolysis of the N-glycosidic bond. Attempts to understand the structural basis for DNA damage recognition by DNA glycosylases have been hampered by the short-lived association of these enzymes with their DNA substrates. To overcome this problem, the design and synthesis of inhibitors that form stable complexes with DNA glycosylases are essential. Complexes can then be studied biochemically and structurally. Toward this end, the Verdine group at Harvard synthesized a pyrrolidine analog that mimics the charged transition state of the enzyme-substrate complex, as shown in Figure 1. When incorporated into double-stranded DNA, they found the pyrrolidine analog (PYR), introduced as the phosphoramidite (1), forms an extremely stable complex with the DNA glycosylase AlkA, exhibiting a dissociation constant in the pM range and potently inhibited the reaction catalyzed by the enzyme.1 Later, the same group in collaboration with international researchers investigated the interaction of this inhibitor with a variety of additional DNA glycosylases. With the exception of uracil DNA glycosylase, all the glycosylases tested bind specifically to PYRcontaining oligonucleotides2 providing an elegant means by which to study a broad range of DNA glycosylases and BER proteins. (Of course, we would be remiss not to mention Vern Schramm when discussing enzymatic transition state analogs and would recommend his excellent review of the subject.3) One might be tempted to think that any abasic analog, such as our dSpacer, (abasic furan 10-1914), might also bind to AlkA. However, the charge is clearly 10
necessary as shown by Verdine’s work.1 When the dSpacer was incorporated rather than the pyrrolidine, the Kd was estimated to be 10,000-fold lower. In any event, it is important to note that pyrrolidine is not directly comparable to our existing abasic phosphoramidite (dR precusor – 10-1924) or dSpacer as the new product will introduce a charge residue. Since the paper that Takeshita et al. published in 19874, the dSpacer/abasic furan (which was introduced a few years later) has been extensively used to study, for example, the fidelity of polymerases when the enzyme encounters an abasic site.223499-30-7 custom synthesis The paper published by Hogg et al.50-81-7 InChIKey in 2006 and several citations in this paper5 are good examples of such research.PMID:30000740 Other information and comparison of various building blocks for the incorporation of abasic lesions can be found in a paper written by Shigenori Iwai.6 Given the importance of analogues involved in base lesions and their repair hold for Glen Research, one might wonder why we haven’t made the Pyrrolidine CE Phosphoramidite ((1) in Figure 1) available before now. It was difficult to provide this analogue because the chemistry used by the Verdine group1 was complex and not really well suited for production purposes. With the development of an alternative synthetic
route, we are happy to provide this new product to the research community studying DNA repair. For the chemists in charge of oligo synthesis, the coupling time of the PYR phosphoramidite should ideally be extended to 5 minutes (tested with 1-H Tetrazole as activator) and the deprotection procedure is standard. We have also carried out accelerated stabili.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