The Skaggs Institute
for Chemical Biology

Scientific Report 2007

Chemical Etiology of the Structure of Nucleic Acids

A. Eschenmoser, R. Krishnamurthy, G.K. Mittapalli, R.R. Kondreddi, Y. Osornio, M. Guerrero, J. Xie

Oligomers Based on 5-Aminopyrimidine–Tagged Oligodipeptide Backbones

In the past year, we continued our studies on the self- and cross-pairing properties of triazine- and 5-aminopyrimidine–tagged oligodipeptides consisting of alternating glutamic (Glu) and aspartic acid (Asp) residues (Fig. 1). We observed that the homododecamer tagged with the 2,4-dioxo-pyrimidine nucleus (^APOO) cross-paired strongly with complementary DNA sequences, whereas the analogous homododecamer tagged with the 2,4-diamino-pyrimidine nucleus (^APNN) cross-paired weakly. This finding was exactly the opposite of that observed in the corresponding oligomers tagged with the complementary 2,4-dioxotrizines (^TOO) and 2,4-diaminotriazines (^TNN) as nucleobases, which we had studied earlier. Therefore, not surprisingly, the intrasystem combination of the two 5-amino-pyrimidine–tagged homo-oligodipeptide dodecamers AspGlu(^APO,O)₁₂ and AspGlu(^APN,N)₁₂ resulted in only very weak intrasystem pairing. The intersystem combination of 2 complementary homobasic oligo-(Asp-Glu)-dipeptide dodecamers, one tagged with the 2,4-dioxopyrimidine nucleus and the other with the 2,4-diaminotriazine nucleus, had reasonably strong intersystem cross-pairing, whereas the inverse combination showed no pairing at all. In the case of the 2 isomeric oxo-amino-5-aminopyrimidine members, (^APON) and (^APNO), experiments indicate that 1 of the 2 isomeric oxo-aminopyrimidine bases can accommodate base pairing via tautomerization.

Fig. 1. Top, Formulas of 5-aminopyrimdine heterocycles. Bottom, Also shown, as a representative example, is the 5-amino-2,4-dioxo–tagged oligomer containing alternating Asp and Glu residues.

The most accessible chemical property that parallels the incongruity of pairing behavior of the 2,4-disubstituted triazines and 5-aminopyrimidines relative to the standard of the canonical nucleobases is the pK_a value (Fig. 2). The juxtaposition points to a correlation between differences in pK_a values (Δ-pK_a) of pairs of complementary bases and the pairing strength of the bases: the smaller the Δ-pK_a value of a pair of complementary 2,4-dioxo and 2,4-diamino pairing partners (compared with the standard difference of about 5 pK_a units for the canonical pair of bases), the weaker is the pairing (in aqueous solution at neutral pH). The trend of this correlation points in the opposite direction of the one described in the literature for Δ-pK_a values of the relative strengths of hydrogen bonds in nonaqueous media.

Fig. 2. Correlation between base-pairing strength with Δ-pKa values of pairs of complementary bases in aqueous solution at neutral pH. Reprinted with permission from Mittapalli, G.K., Osornio, Y.M., Guerrero, M.A., Kondreddi, R.R., Krishnamurthy, R., Eschenmoser, A. Mapping the landscape of potentially primordial informational oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew. Chem. Int. Ed. 46:2478, 2007.

Our observations indicate that 2,4-disubstituted-1,3,5-triazines and 2,4-disubstituted-5-aminopyrimidines, 2 families of heterocycles deemed to be of generational simplicity comparable to that of the canonical nucleobases, yet offering chemically wider opportunities for backbone tagging, are functionally inferior to the family of Watson-Crick bases because of reasons that seem intrinsically chemical. The findings provide a chemical illustration of the view that the canonical nucleobases represent a functional optimum in informational base pairing in aqueous solution.

Oligomers Based on 5-aminopyrimidine–Tagged 2′→3′-Phosphodiester–linked Glyceric Acid Backbones

We are continuing our search for structurally and generationally simpler informational systems, that is, systems considered to have the capability of being assembled from potentially prebiotic source molecules. Recently, we synthesized oligomers derived from a 2′→3′-phosphodiester–linked* glyceric acid backbone that has 2,4-disubstituted 5-aminopyrimidines attached to the carboxyl group via an amide bond at the 5 amino position as recognition elements (Fig. 3), and we are examining the base-pairing properties of the synthesized molecules. We expect that these systems will show base pairing because systems with similar backbone connections, namely 2′→3′-phosphodiester–linked β-D-lyxopyranosyl nucleic acids and 2′→3′-phosphodiester–linked α-D-threofuranosyl nucleic acids, can show Watson-Crick base pairing.

Fig. 3. 5-Aminouracil–tagged 2′→3′-phosphodiester–linked glyceric acid backbone.

We have completed the synthesis of the requisite building block and the machine-assisted automated oligmer synthesis of 2,4-dioxo-5-aminopyrimidine (5-aminouracil)–tagged nucleic acid with a glyceric acid backbone. We have made the oligomer containing six 5-aminouracil units and have begun to explore its base-pairing properties. Preliminary results validate our expectations; we found a strong base pairing between this oligomer and polydeoxyadenosine.

Publications

Egli, M., Pallan, P.S., Pattanayek, R., Wilds, C.J., Lubini, P., Minasov, G., Dobler, M., Leumann, C.J., Eschenmoser, A. Crystal structure of homo-DNA and Nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc. 128:10847, 2006.

Mittapalli, G.K., Kondreddi, R.R., Xiong, H., Munoz, O., Han, B., De Riccardis, F., Krishnamurthy, R., Eschenmoser, A. Mapping the landscape of potentially primordial informational oligomers: oligodipeptides and oligodipeptoids tagged with triazines as recognition elements. Angew. Chem. Int. Ed. 46:2470, 2007.

Mittapalli, G.K., Osornio, Y.M., Guerrero, M.A., Kondreddi, R.R., Krishnamurthy, R., Eschenmoser, A. Mapping the landscape of potentially primordial informational oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew. Chem. Int. Ed. 46:2478, 2007.