Polymerase Synthesis of DNA Containing Iodinated Pyrimidine or 7‐Deazapurine Nucleobases and Their Post‐synthetic Modifications through the Suzuki‐Miyaura Cross‐Coupling Reactions

Abstract

All four iodinated 2′‐deoxyribonucleoside triphosphates (dNTPs) derived from 5‐iodouracil, 5‐iodocytosine, 7‐iodo‐7‐deazaadenine and 7‐iodo‐7‐deazaguanine were prepared and studied as substrates for KOD XL DNA polymerase. All of the nucleotides were readily incorporated by primer extension and by PCR amplification to form DNA containing iodinated nucleobases. Systematic study of the Suzuki‐Miyaura cross‐coupling reactions with two bulkier arylboronic acids revealed that the 5‐iodopyrimidines were more reactive and gave cross‐coupling products both in the terminal or internal position in single‐stranded oligonucleotides (ssONs) and in the terminal position of double‐stranded DNA (dsDNA), whereas the 7‐iodo‐7‐deazapurines were less reactive and gave cross‐coupling products only in the terminal position. None of the four iodinated bases reacted in an internal position of dsDNA. These findings are useful for the use of the iodinated nucleobases for post‐synthetic modification of DNA with functional groups for various applications.

Covalent Modification of Nucleobases using Water‐Soluble Palladium Catalysts

“…The Hocek group reported on the reactivity of ONs containing four different iodonucleoside bases: 5‐IdU, 5‐IdC, 7‐I‐7‐dAz‐dA and 7‐I‐7‐dAz‐dG using the Pd/ADHP catalyst system (Scheme 28). [70] All four iodinated bases could be coupled in modest yield (28–54 %) when the iodonucleoside was incorporated as the 3′‐terminal base of single‐stranded (ss) ONs using a para ‐substituted phenylboronic acid derivative (R 1 B(OH) 2 , Scheme 28a). With a more elaborate and sterically demanding boronic acid coupling partner (R 2 B(OH) 2 ), the 5‐iodopyrimidine bases gave higher yields than did the 7‐iodo‐7‐deazapurine nucleosides.…”

Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties

“…The post-synthesis modification of nucleic acids is a chemical approach in which the nucleoside analogs bearing reactive handles are first incorporated into ODNs and subsequently converted into the desired nucleoside analogs via conjugation chemistry. Various conversion chemistries, such as substitution reactions [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ], click reactions [ 39 , 40 ], amide bond formation [ 41 ], oxime or hydrazone formation [ 42 ], as well as metal-catalyzed cross-coupling reactions [ 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ], have been employed for the post-synthesis modification of canonical nucleosides. In addition, several unnatural nucleoside analogs have also been synthesized via the post-synthesis approach [ 56 , 57 , 58 , 59 ].…”

Purine Nucleosides with a Reactive (β‐Iodovinyl)sulfone or a (β‐Keto)sulfone Group at the C8 Position and Their Polymerase‐Catalyzed Incorporation into DNA

“…Moreover, 8‐amino‐ATP, 8‐azido‐ATP, and 8‐aza‐ATP all produced RNA chain termination of polyadenylation while no primer extension was observed with 8‐Br‐ATP and 8‐Cl‐ATP [27] . Major groove modified 7‐substituted‐7‐deazapurine nucleoside triphosphates are better substrates for DNA polymerases than natural dATP and dGTP as they stabilize DNA duplexes [28–31] …”

“…[27] Major groove modified 7-substituted-7-deazapurine nucleoside triphosphates are better substrates for DNA polymerases than natural dATP and dGTP as they stabilize DNA duplexes. [28][29][30][31] Bioconjugation of the pyrimidine nucleotides bearing reactive groups with an amino acid, peptide or protein have been studied. [32][33][34][35] The Hocek group has cross-linked DNA fragments containing reactive vinylsulfonamide groups to peptides and protein p53.…”