The Skaggs Institute
for Chemical Biology 2004

Scientific Report 2004

Chemical Etiology of the Structure of Nucleic Acids

A. Eschenmoser, R. Krishnamurthy, G.R. Vavilala, J. Nandy, T. George, O. Munoz, H. Xiong

During the past year we worked on the following projects:

C-nucleosidation with (Potentially Natural) Nucleobase Alternatives

We continued our exploration of C-nucleosidation chemistry that began with 5,8-diaza-7,9-dicarba-2,6-diaminopurine (compound 1, “isopurine,” in Fig. 1) and extended our studies to include pyrimidine derivatives (compounds 5–8, Fig. 1) and (modified) purine nucleobases (compounds 9–11, Fig. 1). These bases were selected because they can be derived from potentially prebiotic building blocks. For the C-nucleosidation studies, we used aldosugars, such as threofuranosyl (12 in Fig. 1) and ribofuranosyl (13 in Fig. 1) derivatives, and corresponding iminium ions, derivatives of 3,4-dihydroxy- (14 in Fig. 1) and 3,4-diamino-pyrrolines (15 in Fig. 1), as substrates.

Formation of nucleosides occurred with pyrimidines 7 and 8 and purines 9 and 10. C-nucleosidations with aldosugars as substrates were more sluggish reactions, with lower yields and less stable products than those with the iminium ion counterparts. In some instances (e.g., compounds 1, 9, and 10), we explored C-nucleosidation chemistry with acyclic (aliphatic) iminium ions. C-nucleosides derived from pyrrolinium salts were stable compounds, in contrast to those derived from aliphatic iminium salts. The stability of C-nucleosides correlates inversely with the ease of C-nucleosidation. The investigations done at the Skaggs Institute were complemented by corresponding studies of all 4 members of the 5,8-diaza-7,9-dicarba-purine family (1–4 in Fig. 1) done at the Swiss Federal Institute of Technology (ETH) in Zürich, Switzerland.

Fig. 1. The pyrimidines, purines, and sugar substrates used in the C-nucleosidation studies.

Informational Oligomers Based on Oligoserine Phosphoramidate Backbones

We are investigating oligomers constructed from the monomeric units derived from serine and linked via a phosphoramidate backbone containing a triazine heterocyclic base. We completed the synthesis of an appropriately derivatized serine-triazine monomer unit, and we are searching for conditions for the solid-support synthesis of oligomers.

Structural Properties of (L)-α-threofuranosyl-(3´→2´) Oligonucleotides

We continue to examine the structural properties of (L)-α-threofuranosyl-(3´→2´) oligonucleotides (TNAs). With M. Egli, Vanderbilt University, Nashville, Tennessee, we determined the crystal structure of an A-form DNA duplex of the self-complementary sequence [d(GCGTAT^M)A*d(CGC)]₂ containing a single (L)-α-threofuranosyl-(3´→2´)-adenine (A*) and compared it with the crystal structure of a B-form DNA duplex [d(CGCGAA)T*d(TCGCG)]₂ containing a single (L)-α-threofuranosyl-(3´→2´)-thymine (T*) (T^M = 2´-O-methyl-thymidine). In both A- and B-form duplexes containing a TNA nucleotide, the structure of the TNA unit is similar (C4´-exo conformation), but the TNA unit’s (P–P) distance is more similar to that of an A-form DNA duplex than to that of a B-form DNA duplex (Fig. 2). Therefore, TNA seems to be a good mimic of the A-form of DNA and, by extension, of RNA, rather than a good mimic of the B-form of DNA. This observation offers an explanation as to why TNA hybridizes more strongly with RNA than with DNA and why RNA is a better template for ligating TNA fragments.

Fig. 2. Conformations adopted by TNA and DNA nucleotides in B- and A-form duplexes. A, TNA unit T*7 in B-form. B, DNA unit T20 in B-form. C, TNA unit A*7 in A-form. D, DNA unit A15 in A-form. Asterisks indicate the directions of the backbone chain. Bold arrows indicate the exo (TNA) or endo (DNA) position of the indicated carbon atom.

Publications

Delgado, G., Krishnamurthy, R. Assignment of the ¹H and ¹³C NMR spectra of N2,N6-dibenzoyl-N2,N9-bis(2´ ,3´-di-O-benzoyl-(α)-L-threofuranosyl)-2,6-diaminopurine. Rev. Soc. Quìm. México 47:216, 2003.

Eschenmoser, A. The TNA-family of nucleic acid systems: properties and prospects. Orig. Life. Evol. Biosph. 34:277, 2004.

Pallan, P.S., Wilds, C.J., Wawrzak, Z., Krishnamurthy, R., Eschenmoser, A., Egli, M. Why does TNA cross-pair more strongly with RNA than with DNA? An answer from x-ray analysis. Angew. Chem. Int. Ed. 42:5893, 2003.

Pitsch, S., Wendeborn, S., Krishnamurthy, R., Holzner, A., Minton, M., Bolli, M., Miculka, C., Windhab, N., Micura, R., Stanek, M., Jaun, B., Eschenmoser, A. The β-D-ribopyranosyl-(4´→2´)-oligonucleotide system (“pyranosyl-RNA”): synthesis and resume of base-pairing properties. Helv. Chim. Acta 86:4270, 2003.