Duplex with poly

A Comparison of the Experimental And Calculated Upfleld Shifts Associated With Poly(dA-dT) and Poly(dA-dU) Duplex Formation... 

In the center of the duplex shifts upfield by 0.15 ppm (Table VI, Figure 25) and the thymidine CH3-5 which Is directed towards the major groove shifts upfield by 0.1 ppm (Figure 29). It should be noted that such an upfield shift of the thymidine CH3-5 group was not observed in the intercalation complexes of ethidium (11), proflavine (25), terpyridylplatinum II (11) and nitroaniline dication with poly(dA-dT). The results require that at least one thymidine CH3-5 group project onto the periphery of the anthra-cycline ring system at the intercalation site. 

Poly(U) with 2 -OH substituted by 2 -NH2, and poly(I) and poly(C) with 2 -OH substituted by 2,-0-CO-CH3 l avc not been incorporated, because they failed to form regular duplexes with the complementary homopolynucleotides83, 164). The 2 -NH2 and 2 -0-C0-CH3 substituted homopolymers were devoid of any significant antiviral activity 9, 83),... 

Synthetic peptide-nucleic acids (PNA, Scheme 14C) consisting of poly-N-(2-aminoethyl)glycine which is derivatized with nucleotides, are an interesting hybrid class of compounds, as they are found to form Watson-Crick base pairs with a complimentary peptide-nucleic acid, RNA, and DNA. The polypeptide backbone is achiral but chirality can be induced in the molecule or its assemblies in various ways. Tagging of the peptide-nucleic acid duplex with either L- or D-lysine leads to enantiomorphic structures with opposite CD spectra, analogous to the so-called sergeants-and-soldiers effect for polyisocyanates. When paired with RNA, the peptide-nucleic acid assumes the A-structure typical of RNA (see above). ... 

Hydrophobic interactions exerted by substituents at position 5 of cytosine or uracil enhance stability of DNA/RNA-hybrids (70,71) [163]. Derivatives with longer alkyl chains reduce duplex stability [169], with aminoalkyl residues being an exemption [170]. Above all, ethinyl substitution at position C5 of pyrimidine bases results in significantly increased binding affinity, as shown with binding of modified poly(rU) and poly(rA) [164]. Also, substitution with propinyl showed the same effect (73,74), which was attributed to ji-ji-interactions of the alkinyl substituent with the nucleobase in the 5 -neighbourhood. Oligomers of this type form duplexes with RNA, which can activate RNase-H. Since there is only a minor influence on nuclease resistance, such modifications are preferentially applied in combination... 

Poly(7-deazaguanylic acid) has been prepared by polymerization of 7-deaza-guanosine 5 -diphosphate using polynucleotide phosphorylase from Micrococcus luteus, and its ability to form duplexes with complementary polynucleotides compared with that of poly(G). It is cleaved by ribonuclease T1 and also by nuclease SI, showing that unlike poly(G), it forms no selfstructure in aqueous solution. ... 

Thermal denaturation studies of DNA and DNA-protein complexes are performed on a UV spectrophotometer equipped with temperature controlled cell holders. Melting of the DNA duplex is indicated by a cooperative hyperchromism at 260 nm. Stabilization by Sac7d is most readily observed with poly[d(AT)]-poly[d(AT)] because of its intrinsic low stability, especially in low salt. The UV melting curve of poly[d(AT)] poly[d(AT)] in 0.01 M K2HPO4 is sharp with a Tm of 43.5° (Fig. 9). In the presence of Sac7d, the melting profile of poly[d(AT)]-poly [d(AT)] broadens and the Tm increases by as much as 33°C for solutions with an excess of Sac7d. The observed Tm for the complex depends on the concentration of protein. 

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