Mechanism of degradation of 2'-deoxycytidine by formamide: implications for chemical DNA sequencing procedures

Bioorganic & Medicinal Chemistry
R SaladinoR Negri

Abstract

We describe the reaction of formamide with 2'-deoxycytidine to give pyrimidine ring opening by nucleophilic addition on the electrophilic C(6) and C(4) positions. This information is confirmed by the analysis of the products of formamide attack on 2'-deoxycytidine, 5-methyl-2'-deoxycytidine, and 5-bromo-2'-deoxycytidine, residues when the latter are incorporated into oligonucleotides by DNA polymerase-driven polymerization and solid-phase phosphoramidite procedure. The increased sensitivity of 5-bromo-2'-deoxycytidine relative to that of 2'-deoxycytidine is pivotal for the improvement of the one-lane chemical DNA sequencing procedure based on the base-selective reaction of formamide with DNA. In many DNA sequencing cases it will in fact be possible to incorporate this base analogue into the DNA to be sequenced, thus providing a complete discrimination between its UV absorption signal and that of the thymidine residues. The wide spectrum of different sensitivities to formamide displayed by the 2'-deoxycytidine analogues solves, in the DNA single-lane chemical sequencing procedure, the possible source of errors due to low discrimination between C and T residues.

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Citations

Feb 2, 2002·Chemistry : a European Journal·Lars T Burgdorf, Thomas Carell
Jun 30, 2009·Research in Microbiology·Raffaele SaladinoErnesto Di Mauro
Oct 14, 2004·Chembiochem : a European Journal of Chemical Biology·Raffaele SaladinoErnesto Di Mauro
Jul 9, 2005·Chembiochem : a European Journal of Chemical Biology·Raffaele SaladinoGiovanna Costanzo
Oct 20, 2006·Chembiochem : a European Journal of Chemical Biology·Raffaele SaladinoErnesto Di Mauro
Jun 10, 2003·Chembiochem : a European Journal of Chemical Biology·Raffaele SaladinoErnesto Di Mauro
Apr 20, 2007·Chemistry & Biodiversity·Raffaele SaladinoErnesto Di Mauro
Jul 23, 2005·The Journal of Biological Chemistry·Raffaele SaladinoErnesto Di Mauro
Jun 12, 2012·Chemical Society Reviews·Raffaele SaladinoErnesto Di Mauro

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