Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment

Biochemistry. 2009 Aug 11;48(31):7547-55. doi: 10.1021/bi9006995.


We studied the incorporation of the fluorescent cytidine analogues 1,3-diaza-2-oxophenothiazine (tC) and 1,3-diaza-2-oxophenoxazine (tCo) by human DNA polymerase alpha and Klenow fragment of DNA polymerase I (Escherichia coli). These tricyclic nucleobases possess the regular hydrogen bonding interface of cytosine but are significantly expanded in size toward the major groove. Despite the size alteration, both DNA polymerases insert dtCTP and dtCoTP with remarkable catalytic efficiency. Polymerization opposite guanine is comparable to the insertion of dCTP, while the insertion opposite adenine is only approximately 4-11 times less efficient than the formation of a T-A base pair. Both enzymes readily extend the formed tC(o)-G and tC(o)-A base pairs and can incorporate at least four consecutive nucleotide analogues. Consistent with these results, both DNA polymerases efficiently polymerize dGTP and dATP when tC and tCo are in the template strand. Klenow fragment inserts dGTP with a 4-9-fold higher probability than dATP, while polymerase alpha favors dGTP over dATP by a factor of 30-65. Overall, the properties of tC(o) as a templating base and as an incoming nucleotide are surprisingly symmetrical and may be universal for A and B family DNA polymerases. This finding suggests that the aptitude for ambivalent base pairing is a consequence of the electronic properties of tC(o).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Pairing
  • Cytosine / analogs & derivatives*
  • Cytosine / metabolism*
  • DNA Polymerase I / metabolism*
  • Deoxyadenine Nucleotides / metabolism
  • Deoxyguanine Nucleotides / metabolism
  • Escherichia coli Proteins / metabolism*
  • Geobacillus stearothermophilus / enzymology
  • Humans
  • Nucleic Acid Conformation
  • Nucleic Acid Heteroduplexes / metabolism
  • Oxazines / chemical synthesis
  • Oxazines / metabolism*
  • Phenothiazines / chemical synthesis
  • Phenothiazines / metabolism*


  • 1,3-diaza-2-oxophenothiazin-3-ylacetic acid
  • 1,3-diaza-2-oxophenoxazine
  • Deoxyadenine Nucleotides
  • Deoxyguanine Nucleotides
  • Escherichia coli Proteins
  • Nucleic Acid Heteroduplexes
  • Oxazines
  • Phenothiazines
  • deoxyguanosine triphosphate
  • Cytosine
  • DNA Polymerase I
  • 2'-deoxyadenosine triphosphate