Antiparallel Strand Orientation Research Articles

Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system.

TNAs [(L)-alpha-threofuranosyl oligonucleotides] containing vicinally connected (3'-->2') phosphodiester bridges undergo informational base pairing in antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. Being derived from a sugar containing only four carbons, TNA is structurally the simplest of all potentially natural oligonucleotide-type nucleic acid alternatives studied thus far. This, along with the base-pairing properties of TNA, warrants close scrutiny of the system in the context of the problem of RNA's origin.

Warum Pentose‐ und nicht Hexose‐Nucleinsäuren??. Teil V. (Purin‐Purin)‐Basenpaarung in der homo‐DNS‐Reihe: Guanin, Isoguanin, 2,6‐Diaminopurin und Xanthin

Why Pentose‐ and Not Hexose‐Nucleic Acids? Purine‐Purine Pairing in homo‐DNA: Guanine,Isoguanine, 2,6‐Diaminopurine, and XanthineThis paper concludes the series of reports in this journal [1–4] on the chemistry of homo‐DNA, the constitutionally simplifie dmodel system of hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems stidued in our laboratory as potentially natural‐nucleic‐acid alternatives in the context of a chemical aetiology of nucleic‐acid structure. The report describes the synthesis and pairing properties of homo‐DNA oligonucleotides which contain as nucleobases exclusively purines, and gives, together with part III of the series [3], a survey of what we know today about purine‐purine pairingin homo‐DNA. In addition, the paper discusses those aspects of the chemistry of homo‐DNA which, we think, influence the way how some of the structural features of DNA (and RNA) are to be interpreted on a qualitative level.Purine‐purine pairing occurs in the homo‐DNA domain in great variety. Most prominent is a novel tridentate Watson‐Crick pair between guanine and isoguanine, as well as one between 2,6‐diaminopurine and xanthinone, both giving rise to very stable duplexes containing the all‐purine strands in antiparallel orientation. For the guanine‐isoguanine pair, constitutional assignment is based on temperature‐dependent UV and CD spectroscopy of various guanine‐ and isoguanine‐containg duplexes in comparison with duplexes known to be paired in the reverse guanine is replaced by 7‐carbauguanine. Isoguanine and 2,6‐diaminopurine also have the capability of self‐pariring in the reverse‐Hoogsteen mode, as previously observed for adenine and guanine [3]. In this type of pairing, the interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine‐purine combinations.Watson‐Crick pairing of isoguanine with guanine demands the former to participate in its 3H‐tautomeric form; hitherto this specific tautomer had not been considered in the pairing chemistry of isoguanine. Whereas (cumulative) purine‐purine pairing in DNA (reverse‐Hoogsten or Hoogsteen) seems to occur in triplexes and tetrapalexes only, its occurrence in duplexes in a characteristic feature of homo‐DNA chemistry. The occurrence of purine‐purine Watson‐Crick base pairs is probably a consequence of homo‐DNA's quasi‐linear ladder structure [1][4]. In a double helix, the distance between the two sugar C‐atoms, on which a base pair is anchored, is expected to be constrained by the dimensions of the helix; in a linear duplex, however, there would be no restrictions with regard to base‐pair length. Homo‐DNA's ladder‐like model also allows one to recognize one of the reasons why nucleic‐acid duplexes prefer to pair in antiparallel, rather than parallel strand orientation: in homo‐DNA duplexes, (averaged) backbone and base pair axes are strongly inclined toward one another [4]; the stronger this inclination, the higher the preference for antiparallel strand orientation is expected to be (Fig. 16).In retrospect, homo‐DNA turns out to be one of the first artificial oligonucleotide systems (cf. Footnote 65) to demonstrate in a comprehensive way that informational base pairing involving purines and pyrimidines is not a capability unique to ribofuranosyl systems. Stability and helical shape of pairing complexes are not necessary conditions of one another; it is the potential for extensive conformational cooperativity of hte backbone structure with respect to the constellational demands of base pairing and base stacking that determines whether or nor a given type of base‐carrying backbone structure is an informational pairing system. From the viewpoint of the chemical aetiology of nucleic‐acid structure, which inspired our investigations on hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems in the first place, the work on homo‐DNA is only an extensive model study, because homo‐DNA is not to be considered a potential natural‐nucleic‐acid altenratie. In retrospect, it seems fortunate that the model study was carried out, because without it we could hardly have comprehended the pairing behavior of the proper nucleic‐acid alternatives which we have studied later and which will be discussed in Part VI of this series.The English footnotes to Fig. 1–49 provide an extension of this summary.

Pyranosyl‐RNA (‘p‐RNA’): NMR and Molecular‐Dynamics Study of the Duplex Formed by Self‐pairing of Ribopyranosyl‐(C‐G‐A‐A‐T‐T‐C‐G)

AbstractThe solution structure of the duplex formed by self‐pairing of the p‐RNA octamer β‐D‐ribopyranosyl‐(2′→4′)‐(CGAATTCG) was studied by NMR techniques and, independently, by molecular‐dynamics calculations. The resonances of all non‐exchanging protons, H‐bearing C‐atoms, P‐atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson‐Crick pairing with antiparallel strand orientation. The dihedral angles β and ϵ in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base‐pair axis forms an angle of ca. 40° with the backbone. The resulting interstrand π‐π stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p‐RNA duplex. A 1000‐ps molecular‐dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. For the backbone torsion angle ϵ, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle β, a systematic difference of ca. 25° remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.

Homooligomeric dA.dU and dA.dT sequences in parallel and antiparallel strand orientation: consequence of the 5-methyl groups on stability, structure and interaction with the minor groove binding drug Hoechst 33258.

Oligodeoxyribonucleotides containing dA.dU base combinations were shown to form parallel stranded DNA. CD spectra and hyperchromicity profiles provide evidence that the structure is very similar to that of a related parallel stranded dA.dT oligomer. Thermal denaturation studies show that these parallel dA.dU sequences are significantly less stable than their dA.dT analogues in either antiparallel or parallel stranded orientations. The stabilizing effect of the 5-methyl group is similar for parallel and antiparallel sequences. The minor groove binding drug Hoechst 33258 binds with similar affinity to APS dA.dT and APS dA.dU sequences. However, binding to the PS dA.dT hairpin is significantly impaired as a consequence of the different groove dimensions and the presence of thymine methyl groups at the binding site. This results in an 8.6 kJmol-1 reduced free energy of binding for the PS dA.dT sequence. Replacement of the bulky methyl group with a hydrogen (ie. T-->U) results in significantly stronger Hoechst 33258 binding to the parallel dA.dU sequences with a penalty of only 4.1 kJmol-1. Our data demonstrate that although Hoechst 33258 detects the altered groove, it is still able to bind a PS duplex containing dA.dU base pairs with high affinity, despite the large structural differences from its regular binding site in APS DNA.