Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

Abstract

The physical and chemical factors that allow DNA to perform its functions in the cell have been studied for several decades. Recent advances in the synthesis and manipulation of DNA have allowed this field to move ahead especially rapidly during the past fifteen years. One of the most common chemical approaches to the study of interactions involving DNA has been the use of DNA base analogues in which functional groups are added, deleted, blocked, or rearranged. Here we describe a different strategy, in which the polar natural DNA bases are replaced by nonpolar aromatic molecules of the same size and shape. This allows the evaluation of polar interactions (such as hydrogen bonding) with little or no interference from steric effects. We have used these nonpolar nucleoside isosteres as probes of noncovalent interactions such as DNA base pairing and protein - DNA recognition. We have found that, while base-pairing selectivity does depend on Watson - Crick hydrogen bonding in the natural pairs, it is possible to design new bases that pair selectively and stably in the absence of hydrogen bonds. In addition, studies have been carried out with DNA polymerase enzymes to investigate the importance of Watson - Crick hydrogen bonding in enzymatic DNA replication. Surprisingly, this hydrogen bonding is not necessary for efficient enzymatic synthesis of a base pair, and significant levels of selectivity can arise from steric effects alone. These results may have significant impact both on the study of basic biomolecular interactions and in the design of new, functionally active biomolecules.

Incorporation of Zebularine from its 2′-Deoxyribonucleoside Triphosphate Derivative and Activity as a Template-Coding Nucleobase

“…This suggests that something other than the energetics of the newly-formed base pair accounts for the increased incorporation of dZTP opposite guanine, compared to dCTP. A similar behavior has been observed when other nucleoside analogs (35) and non-polar isosteres of nucleobases (36) were incorporated into DNA, indicating that the geometry rather than thermodynamic stability is important for DNA polymerase activity.…”

Synthesis and Properties of Size-Expanded DNAs: Toward Designed, Functional Genetic Systems

“…41,42 The key step for these C-glycosides was glycoside bond formation (Scheme 2); in the presence of Pd(OAc) 2 and AsPh 3 , the iodinated base analogues were added via Heck reaction onto a silyl-protected dihydrofuran. 43 The syntheses of three yDNA nucleosides have also been reported recently.…”

Solution Structure of a Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate in DNA

“…6 Since hydrogen bonds are apparently dispensable in maintaining natural enzyme activity, we proposed that the fidelity of DNA replication might arise in large part from steric matching of bases within a tightly confined active site. 3,7,8 This hypothesis was criticized by suggesting that the reason that F behaved as such an effective mimic of T was that it actually did form robust hydrogen bonds with adenine.9 After this, several experiments and calculations with this fluorinated analogue and related compounds have concluded that C-F…H-N hydrogen bonding character is quite poor in this context, especially in the aqueous environment.10 -18 Nonetheless, a clearer way to avoid the issue of possible hydrogen bonds between F and A is to replace adenine with a nonpolar isostere, as was done for thymine. To this end, we chose a 4-methylbenzimidazole replacement used for adenine (Z) and studied its ability to be replicated opposite F. 19 , 20 It was found, interestingly, that this pair was an efficient substrate for the Klenow polymerase, and it was processed with significant levels of selectivity.…”