Synthesis of DNA Dumbbell Based Inhibitors for the Human DNA Methyltransferase Dnmt1

Abstract

Dumbbells that block: Dnmt1 is a crucial enzyme in maintaining the methylation pattern of genes and as such is a critical element of the epigenetic programming process. DNA dumbbell constructs have been developed that inhibit Dnmt1 and have potential in the regulation of DNA methylation patterns in cells (see scheme; SAM=S‐adenosylmethionine, Fl=Cy3 fluorescence label, CN=5‐azadC, C‐Me=5‐methyldC).

Mechanism‐Based Inhibitor of DNA Cytosine‐5 Methyltransferase by a SNAr Reaction with an Oligodeoxyribonucleotide Containing a 2‐Amino‐4‐Halopyridine‐C‐Nucleoside

“…Therefore, DNMT binds to ds-F P:Gm ore efficiently than ds-F C:Gi nt he presence or absence of any cofactor. However,t he band shifts were different between SAM and SAH/no cofactor ( Figure 2B,l anes 5, 8a nd 2, 6,7,9,10). To elucidate the difference in migration, the same experiments were performed by using native PAGE ( (Figure S3 B, lane 5).…”

“…A modified ODN containing d F C in the CpG sequence still has low reactivity and needs methylation by SAM for its inhibition of DNMTs. Chemical incorporation of d N C into ODN is intractable . Therefore, the development of new lead nucleic acid drugs containing nucleoside analogues that are more chemically stable, more reactive with DNMTs, and form a stable complex with DNMTs are needed as oligonucleotide therapeutics and molecular probes for studies of epigenetics.…”

“…[4] Therefore, inhibition of human DNMT is an effective strategy to treat various cancers. [5] Basemodified nucleoside analogues,s uch as 5-aza-2'-deoxycytidine (d N C), [6] 5-fluoro-2'-deoxycytidine (d F C) [7] and zebularine, [8] act as suicide inhibitorso fDNMTsafter incorporation into genomic DNA at CpG sites. In DNA, the modified nucleobase forms acovalent bond with the Cys residue.…”

Synthesis of 2‐Amino‐4‐Fluoropyridine‐C‐Nucleoside Phosphoramidite for Incorporation into Oligonucleotides

“…Therefore, inhibition of human DNMT is an effective strategy for treating various cancers (Ehrlich, 2002;Esteller 2002;Gilbert et al, 2004;Herman & Baylin, 2003). Base-modified nucleoside analogues, such as 5-aza-2 -deoxycytidine (d N C) (Christman, 2002;Kuch, Schermelleh, Manetto, Leonhardt, & Carell, 2008;Momparler, Momparler, & Samson, 1984) and 5fluoro-2 -deoxycytidine (d F C) (Chen et al, 1991;Osterman, DePillis, Wu, Matsuda, & Santi, 1988), act as suicide inhibitors of DN-MTs after incorporation into genomic DNA at CpG sites. In DNA, the modified-nucleobase forms a covalent bond with the Cys residue (Klimašauskas, Kumar, Roberts, & Cheng, 1994;Santi, Norment, & Garrett, 1984;Zhou et al, 2002).…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…5-Methyl-dC containing oligonucleotides are substrates for DNA methyltransferase enzymes, and the 5-aza-dC containing dumbbell was able to trap the methyltransferase Dnmt1 by forming a covalent crosslink with it. 173 Pyrrolo-dC modified by the addition of alkynyl side chains have been used in Click reactions with azido-coumarin in oligonucleotides, resulting in highly fluorescent probes. 174 Alkynylated pyrrolo-dC is more stabilising in a duplex than the parent or the analogous saturated nucleotide.…”