Table 1.

Selected kinetic data for effects of phosphodiester linkage alteration in RNA and DNA on pol II transcription

LinkageIncorporationkpol, min−1Kd,app, μMkpol/Kd,app, μM−1·min−1Relative efficiency*Discrimination
Wild typeATP750 ± 21090 ± 208.3 ± 3.01(4.4 ± 1.8) × 105
UTP0.015 ± 0.003800 ± 60(1.9 ± 0.4) × 10−51
Primer mutantATP15 ± 1250 ± 400.06 ± 0.010.007 ± 0.003(1.1 ± 0.2) × 105
UTP(4.5 ± 0.2) × 10−4800 ± 90(5.6 ± 0.7) × 10−70.029 ± 0.007
Template mutantATP17 ± 1530 ± 600.032 ± 0.0040.004 ± 0.003910 ± 200
UTP0.13 ± 0.013,700 ± 700(3.5 ± 0.7) × 10−51.8 ± 0.5
  • * Relative efficiency = (kpol/Kd,app)ATP, 2’-5′/(kpol/Kd,app)ATP, 3′-5′ or (kpol/Kd,app)UTP, 2’-5′/(kpol/Kd,app)UTP, 3′-5′.

  • Discrimination = (kpol/Kd,app)ATP/(kpol/Kd,app)UTP.

  • The scaffolds with 2′–5′ linkage alteration are shown in Figs. 2A and 3C (10A scaffold), and depicted in Fig. 7.