Fig. 4.21 Schematic illustration of a PNA (left) and an antiparallel PNA double strand based on heterochiral alanyl-oligomers with complementary G-C base sequences [64].

to the well known double helical structure. Sometimes, the hybridization is hampered by the intramolecular structuring of the single stranded DNA itself. Long single-stranded DNA and RNA can have considerable secondary structures such as loops or bulbs that can prevent its interaction with the complementary oligonucleotides [61]. Shorter oligonucleotides however are normally unstructured and only obtain their specific fold in the context of the double helix. A variety of DNA analogs with similar pairing and folding properties have been designed based both on natural (nucleotides and peptides) as well as unnatural backbones (hydrocarbon skeletons) [62, 63].

For example, peptide nucleic acids (PNAs) are oligonucleotide mimics in which the sugar phosphate backbone is replaced with an N-(1-aminoethyl)glycine polymer carrying A, G, C, and T nucleobases via methylene carbonyl linkages (Fig. 4.21). These strands by themselves are not orderly structured but consist as mixtures of various conformations (e.g. cis/trans amide rotamers). However, they possess the same hybridization properties as normal DNA or RNA, forming stable duplexes based on Watson-Crick base pairing either with another PNA (Fig. 4.21) or with both types of nucleotides. In this context PNAs might have some promise for antisense gene therapy or as DNA probes [64].

Fig. 4.22 b-Peptides with attached nucleobases can form stable duplexes via helix aggregation through antiparallel Watson-Crick base pairing.

Also b-peptides [65] can function as a foldamer scaffold for the formation of self-assembled duplexes. Gellman and Diederichsen [66] designed a b-peptide with nucleobases attached at every third position, which can form a 14-helix. The other positions were assigned with b-homolysine in order to increase solubility in

Fig. 4.23 A polymer formed by ring-opening metathesis from a bis-norbornene derivative with a rigid ferrocene bridge, resembles DNA by having a double helical structure with similar geometric parameters as natural DNA (A) [68]. STM experiments on HOPG confirm double helix formation (B) [68].

aqueous media and 2-aminocyclohexane carboxylic acid (ACHC), which should strongly promote the 14-helix formation. The single strands are still very flexible in solution. However, this conformation acts as a scaffold for the presentation of the nucleobases on one side of the helix. Watson-Crick base pairing between two complementary strands then leads to stable duplexes (Fig. 4.22), which were verified by ESI mass spectrometry and temperature dependent UV and CD spectrometry even though the exact conformations and structures of either the single or the double strands have not yet been determined. For example, an equimolar mixture of complementary oligomers, containing the nucleobase sequences ATCA and TGAT, forms a duplex of significant stability (Tm = 44 °C). In order to determine the utility of hydrogen-bond-mediated base pairing for the duplex formation, methylated guanine nucleobases were synthezised and incorporated into the b-peptide helix. These modified nucleobases are no longer able to dimerize over the Watson-Crick site, so that no interaction of the two helices was detected by temperature-dependent UV spectroscopy. Also the CD spectra, recorded at low temperature, gave no indication for base-paired double strands. These measurements confirm the need for free Watson-Crick sites for base pairing. Helical b-peptides by themselvess can self-assemble in water, but in this case rather un-specific aggregates of unknown composition and structure are formed [67].

An interesting DNA analog, albeit remote, based on a complete artificial skeleton was described by Luh [68]. A bis-norbornene derivative with an incorporated ferrocene unit was polymerized using ring opening metathesis leading to a double stranded polymer with an average of 29 repeat units (Fig. 4.23). As scanning tunneling microscopy showed this double strands can adopt several structures one being a classical double helix (besides a supercoiled and a ladder structure, Fig. 4.23 B). This double helix has geometric parameters very similar to the natural DNA as far as for example the number of monomeric units per pitch or the spacing between them is concerned. However, according to molecular mechanics calculations this double helical structure is energetically less favorable compared to the supercoiled or ladder structure.

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