Double mismatched

Fig. 7 Fluorescence intensity of the PNA/DNA hybrid vs. separation temperature. Fluorescein-labeled PNA probes with complementary 3 sequence. Voltage 20 kV. Detection LIF 488/520 nm. Buffer IX TBE/30% formamide (pH 8.3). The following M13 probes were used 5 -fluorescein-00-TTT TCC CAG TCA CGA (perfect match), 5 -fluorescein-OO-TTT TCC CAG GCA CGA (single mismatch), 5 -fluo-rescein-OO-TTT TCA CAG GCA CGA (double mismatch). (From Ref. 37.)...

Another class of DNA-binding proteins are the polymerases. These have a nonspecific interaction with DNA because the same protein acts on all DNA sequences. DNA polymerase performs the dual function of DNA repHcation, in which nucleotides are added to a growing strand of DNA, and acts as a nuclease to remove mismatched nucleotides. The domain that performs the nuclease activity has an a/P-stmcture, a deep cleft that can accommodate double-stranded DNA, and a positively charged surface complementary to the phosphate groups of DNA. The smaller domain contains the exonuclease active site at a smaller cleft on the surface which can accommodate a single nucleotide. 

The reaction of methyl 4-formyl-2-mcthylpentanoate and the chiral (Z)-2-butenylboronate clearly shows 52b-103, however, that the chiral auxiliary is not sufficiently enantioselective to increase the diastereoselectivity to >90% in either the matched [( + )-auxiliary] or mismatched [(—)-auxiliary] case. This underscores the requirement that highly enantioselective chiral reagents be utilized in double asymmetric reactions. 

Dimethylphenylsilyl-2-propenylboronate 7 is more enantioselective (81-87% ee with achiral aldehydes) than the 2-[cyclohexyloxy(dimethyl)silyl] compound 8 (64-72% ee), and consequently the former generally gives better results especially in mismatched double asymmetric reactions. Nevertheless, the examples show that appreciable double diastereoselection may be achieved with both reagents in many cases. 

Evidently, the intrinsic diastereofacial selectivity preference of 13 is too great for the chiral 2-butenylboronate to dominate the stereochemical course of this reaction. A second unsuccessful attempt at a demanding case of mismatched double diastereoselection has been reported by Burgess87. 

The data summarized in Section 1.3.3.3.3.2.3. established that a-chloro-2-propenylboronate 2 is more enantioselective than l9,32a b. It is not surprising, therefore, that the reactions of 2 and chiral aldehydes exhibit greater diastereoselectivity, particularly those cases involving mismatched double diastereoselection. This point is demonstrated by the reactions with (i )-2,3-[isopropylidenebis(oxy)]propanal. 

The matched double asymmetric reactions with (7 )-l and (a.R,S,S)-2 provide the (S,Z)-diastereomer with 94% and 96% selectivity, while in the mismatched reactions [(S)-l and (aS,R,R)-2] the (S.Z)-diastereomer is obtained with 77% and 92% selectivity, respectively. Interestingly, the selectivity of the reactions of (/ )-2,3-[isopropylidenebis(oxy)]propanal and 2 is comparable to that obtained in reactions of (7 )-2,3-[isopropylidenebis(oxy)]propanal and the much more easily prepared tartrate ester modified allylboronates (see Table 7 in Section 1.3.3.3.3.1.5.)41. However, 2 significantly outperforms the tartrate ester allylboronates in reactions with (5)-2-benzyloxypropanal (Section 1.3.3.3.3.1.5.), but not the chiral reagents developed by Brown and Corey42-43. 

By way of comparison, the mismatched double asymmetric reaction of (5)-2-methylbu-tanal and E)- -methoxy-2-butenylboronate (5)-4 exhibits much greater selectivity. Dia-stereomers 9 (ca. 95%) and 7 (ca. 5%) are the only observed products, indicating that the diastereofacial selectivity of the 9/10 pair is >95 5. Here again, the small amount of 7 that was obtained (5 %) probably derives from the reaction of (S)-2-methylbutanal and the enantiomeric reagent (/ )-4, since (S)-4 is not enantiomerically pure (ca. 90% ee). 

The greater diastereofacial selectivity of 4 is also evident in the attempted mismatched double asymmetric reactions of 3 and 4 with aldehydes 11 and 15. which have greater intrinsic diastereofacial preferences than (S)-2-methylbutanal. 

The reactions with (25,35,45,55)-5-(tm-butyldimethylsilyloxy)-3-(4-methoxyphenylmethoxy)-2,4-dimethylheptanal (15) are particularly informative reagent (5)-3 is incapable of overriding the intrinsic diastereofacial preference of 15, and the normal Felkin product 17 is obtained with >95% selectivity. In contrast, reagent-controlled mismatched double diastereoselectivity is evident in the reaction with (5)-4 that provides 16 as the major component of a 73 22 5 mixture. The minor product 18 apparently derives from a reaction with the contaminating (/ )-4, since (5)-4 that was used is not enantiomerically pure. 

Reagent 4 is the most selective ( )-2-butenylboron reagent available for application in demanding cases of mismatched double diastcrcosclcction. considerably more so than the chiral reagents discussed in Section 1.3.3.3.3.1.5. It is noted that the mismatched double asymmetric reactions are often very slow, particularly in the most stereochemically demanding eases, and the reactions of 11 and 15 with 4 are thus performed at 4 kbar pressure12 25. 

Difficulties have been encountered in mismatched double asymmetric reactions involving (a-S,S,S)-5, as illustrated by the reaction with 21. 

After 12 hours at 4 kbar. this reaction provided only 35% of a 63 27 mixture of 22 and a compound which was tentatively assigned structure 23. It is assumed that 23 derives from epimerization of 21 prior to reaction with (aS,S,S)-5l0b. Whether this stereochemical assignment is correct or not, this result shows that 5 may have problems with configurationally labile aldehydes in demanding cases of mismatched double diastereosclcction. For further examples of double asymmetric induction with 5 or related reagents, see refs 31, 34 and 47. 

An example of double asymmetric induction has been reported. The resolved enantiomers of rac-4 have been converted to the aluminum enolates and reacted at —78 °C with enantiomer-ically pure ter/-butyl (S)-2-fonnyl-l-pyrrolidine carboxylate46. A comparison of the two reactions reveals that the reaction pair leading to the (5Fe,/ ,5)-product is matched while the alternative reaction pair is mismatched. 

Indeed, the combination of the aldehyde 1 with the (S)-enolate 2 delivers the diastereomers 3a and 3b in excellent selectivity (>100 1, matched pair ). On the other hand, a 1 30 ratio of 4 a/4 b is found in the corresponding reaction of the (2 )-enolate 2. Although the selectivity in the latter case ( mismatched pair ) is distinctly lower, the reliability of this chiral enolate 2 provides a degree of induced stereoselectivity which is sufficient for practical applications ( double diastereodifferentiation )29. The stereochemical outcome is largely determined by the chirality of the enolate in that the (S)-enolate 2 attacks the aldehyde almost exclusively from the Re-face whereas the (/ -enolate adds preferably to the Si-face of the carbonyl group in the aldehyde. 

Polynucleotides. Polynucleotides are potent interferon inducers. A mismatched, double-stranded synthetic polyribonucleotide ampligen and the double-stranded acids, polyadenylic-polyuridylic acid and polyinosinic-polycytidylic acids have been widely studied for cancer therapy(ii). Although these materials elicit excellent activity with murine rodents, therapeutic effects are dramatically decreased within primates. 

In the perfectly paired double strand 22, the yield of product PGgg> which indicates the amount of charge that has reached the hole trap GGG, is 68%. But if the intermediate G C base pair is exchanged by a G T mismatch, the efficiency of the charge transport drops to 23%. With an abasic site (H) opposite to G the hole transport nearly stops at this mismatched site (Fig. 15). We have explained this influence of a mismatch on the efficiency of the charge transport by a proton transfer from the guanine radical cation (G2 +)... 

Fig. 15 Influence of mismatches on the efficiency of hole transfer through double strands 23 and 24 where the cytidine (C) is exchanged by thymidine (T) and an abasic site (H), respectively. In 25 guanosine is exchanged by N-methylguanosine (see Scheme 6), and C by an abasic site (H)...

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