Esther Yeheskiely

A Novel N‐(Pyrrolidinyl‐2‐methyl)glycine‐Based PNA with a Strong Preference for RNA over DNA

A novel, N-(pyrrolidinyl-2-methyl)glycine-based (Pmg-based) PNA is introduced. The synthesis of the backbone was accomplished in good yield, starting from prolinol. Thymine (S)- and (R)-Pmg and adenine- and cytosine-derived (R)-Pmg monomers were prepared. Five different fragments − two with either the (R) or the (S) isomer of the thymine Pmg monomer, two oligomers with two consecutive (R)- or (S)-thymine Pmg units, and fully modified (R)-Pmg decamer − were assembled on a solid support. UV thermal melting experiments with complementary DNA and RNA were performed in order to determine the effects of conformational restriction, steric hindrance, and chirality on the duplex stability. It was found that the (R)-Pmg-containing PNAs bound better to DNA and RNA than those containing the (S)-Pmg isomer and that both (S)- and (R)-Pmg-containing PNAs preferentially bound to complementary RNA with a selectivity higher than that of 2-(aminoethyl)glycine (Aeg) PNA. However, even (R)-Pmg-containing oligomers showed poorer duplex stability than nonmodified Aeg-PNA, while no detectable binding either to the DNA or to the RNA was observed with the fully modified (R)-Pmg decamer. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

Cationic peptides that increase the thermal stabilities of 2'-O-MeRNA/RNA duplexes but do not affect DNA/DNA melting.

Several different cationic nonapeptides have been synthesized and investigated with respect to how they can influence the thermal melting of 2′‐O‐methylRNA/RNA and DNA/DNA duplexes. Each peptide has a C‐terminal L‐phenylalanine unit and is otherwise uniformly composed of a sequence of a specific basic D‐amino acid that in most cases will be largely charged at neutral pH. These N‐terminal octamer stretches are composed variously of the amino acids D‐lysine, D‐diaminobutyric acid (D‐Dab), D‐diaminopropionic acid (D‐Dap), or D‐histidine. None of the peptides substantially affected the thermal melting of DNA/DNA duplexes, which was in sharp contrast with their effects on 2′‐O‐methylRNA/RNA duplexes. In particular, the peptides based on diaminopropionic and diaminobutyric acid units had strong positive effects on the melting temperatures of the 2′‐O‐methylRNA duplexes (up to 16 °C higher with 1 equivalent of peptide) at pH 7, whereas at pH 6 the effect was even more drastic (ΔTm up to +25 °C). The shorter R groups of the Dap and Dab groups appear to have a better length than lysine for enhancement of the thermal melting of the 2′‐O‐methylRNA/RNA duplex, an effect that is more pronounced at lower pH but substantial even at pH 7, although the Dap derivative is not likely to be fully protonated. The dramatic difference between the influence, or lack thereof, on the 2′‐O‐methylRNA/RNA and the DNA/DNA thermal meltings suggest that, although electrostatic interactions probably play a role, there is another major and structurally dependent component influencing the properties of the duplexes. This is also seen in the observation that the oligo‐Dap and oligo‐Dab peptides give greater melting point enhancements than both the lysine peptide (with a longer side chain) and a β‐linked Dap peptide with a shorter side chain and a longer backbone.

Suppression of Exonucleolytic Degradation of Double-Stranded DNA and Inhibition of Exonuclease III by PNA

Abstract Degradation of double-stranded DNA by Exonuclease III in the presence of complementary anti-parallel PNA was studied. It was found for the first time that the PNA suppresses the degradation of dsDNA in a sequence-specific manner as well as inhibits the activity of Exonuclease III in a non-specific way.

SYNTHESIS AND HYBRIDIZATION OF NOVEL CHIRAL PYRROLIDINE BASED PNA ANALOGUE

Four different PNA fragments containing units of either the R- or S- isomer of N-(2-pyrrolidine-methyl)-N-(thymine-1-acetyl)-glycine (Pmg) were synthesized on a solid support. UV thermal melting experiments with complementary RNAs were performed and it was found that R-Pmg containing PNAs bind better to RNA than those containing the S-Pmg units.

SYNTHESIS AND REACTIVITY OF NUCLEOSIDE SULFILIMINES

Treatment of 3′- and 5′-protected deoxycytidine and deoxyadenosine with bis-[α,α-bis(trifluoromethyl)benzyloxy]diphenylsulfur resulted in the formation of the corresponding 4-N- and 6-N-diphenylsulfilimine derivatives in good yields. The 4-N- and the 6-N-dimethylsulfilimines of these nucleosides were obtained using DMSO/trifluoroacetic anhydride. These dimethyl- and diphenylsulfilimine derivatives were found to have characteristic UV absorbances at 284-296 nm. Stability tests of the nucleoside dimethylsulfilimine and diphenylsulfilimine under the conditions commonly used in oligonuclotide chemistry by the H-phosphonate approach were executed, and possible applications of these compounds have been discussed.