Bi-stranded, multisite replication of a base pair between difluorotoluene and adenine: confirmation by 'inverse' sequencing

Background: The nonpolar nucleoside of difluorotoluene (F) was previously found to behave similarly to thymidine in single-site deoxynucleoside triphosphate (dNTP) insertion experiments with the Klenow fragment (KF) of DNA polymerase I. Further study was needed, first to see whether F-A base pairs could be replicated in more than one sequence context; second to investigate whether specific base pair replication occurs in the presence of four dNTPs; and third to confirm the presence of F in a replicated DNA strand. Results: A primer bound to a template strand containing eight F residues was extended by KF using the four natural dNTPs at 20 mu M. Similarly, the complement (containing eight adenines) was extended using dATP, dGTP, dCTP and dFTP, Comparison of the new strands to authentic strands using standard and 'inverse' chemical sequencing showed identical composition within +/- 5%. Conclusions: The results confirm that F in a template strand encodes the insertion of dATP and that adenine in a template encodes the insertion of dFTP with good specificity in at least six different nearest neighbor contexts. The results confirm that analog F behaves similarly to thymidine despite its poor hydrogen-bonding ability.