Volume 4, Issue 2, Pages 281-286 (August 1999) The dinB Gene Encodes a Novel E. coli DNA Polymerase, DNA Pol IV, Involved in Mutagenesis  Jérôme Wagner, Petr Gruz, Su-Ryang Kim, Masami Yamada, Keiko Matsui, Robert P.P Fuchs, Takehiko Nohmi  Molecular Cell  Volume 4, Issue 2, Pages 281-286 (August 1999) DOI: 10.1016/S1097-2765(00)80376-7

Figure 1 DinB Has a Template-Directed DNA Polymerase Activity with No Associated 3′ to 5′ Exonuclease Activity Specificity of nucleotide incorporation by HT-DinB was investigated by reacting 30 nM of the specified substrates with 10 nM of pure HT-DinB and with or without dNTP as specified. In the right panel, the activity of HT-DinB (10 nM) on a 3′ end–mismatched primer/template duplex (*31/44; 50 nM) was compared to the one of Klenow Fragment (KF) exo− (2 nM) and KF exo+ (2 nM) DNA polymerases in the absence of added dNTP. Insert: SDS-PAGE profile of purified HT-DinB protein (10 μg loaded). Molecular Cell 1999 4, 281-286DOI: (10.1016/S1097-2765(00)80376-7)

Figure 2 DinB Is a Strictly Distributive Polymerase Processivity of HT-DinB was assayed on a single-stranded circular DNA (pUC118ss) primed with a 5′ radiolabeled 24 primer. A fixed amount of substrate (50 nM) was incubated with decreasing amounts of polymerase, as specified. At equimolar concentrations of substrate and HT-DinB (50 nM, lane 4) or at higher substrate to enzyme ratio (lanes 5 and 6), the major product formed results from the addition of only one nucleotide. At the lowest HT-DinB concentration tested, no more polymerase activity could be detected (lane 7). Molecular Cell 1999 4, 281-286DOI: (10.1016/S1097-2765(00)80376-7)

Figure 3 DinB Elongates Misaligned Rather than Terminal Mismatched Primer/Template Substrates Perfectly matched substrate (1 pmol, *20C/46; left panel) was incubated with 1 pmol of HT-DinB (lane 1), 0.1 pmol of KF exo− (lane 2), or 0.1 pmol of KF exo+ (lane 3). Each reaction produces full-length products, and one can note the particular propensity of KF exo− to add nontemplated nucleotides at the 3′ end of the product (lane 2; 47 nt and 48 nt long products). On the right are presented elongations of a 3′ terminal mismatched primer/template substrate (*20G/46; lanes 4–6) by the same polymerases. Elongation profiles generated by KF enzymes do not differ dramatically from the one obtained with the matched substrate (lanes 2 and 3). In marked contrast, HT-DinB (lane 4) produced a 1 nt shorter product when compared to the one observed with the matched substrate (lane 1). Sequence analysis of this product revealed that it results from the elongation of a structure formed by pairing of the 3′ terminal primer base (G) with the next template base (C), thus generating a bulged, but 3′-matched primer/template substrate as depicted in the insert. Molecular Cell 1999 4, 281-286DOI: (10.1016/S1097-2765(00)80376-7)

Figure 4 The DinB003 Mutant Lacks Primer/Template Extension Activity Purified HT-DinB003 protein (insert) was assayed for DNA polymerase activity in the same conditions as in Figure 1 except that the concentration of protein was doubled. With the exception of lanes 2 (*25/44) and 3 (*27/44) where very low levels of 1–2 nt incorporation could be detected, no DNA polymerase activity could be associated to HT-DinB003. Insert: SDS-PAGE profile of purified HT-DinB003 protein (10 μg loaded). Molecular Cell 1999 4, 281-286DOI: (10.1016/S1097-2765(00)80376-7)