Peptide Nucleic Acid with Double Face: Homothymine-Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA2:DNA Triplex.

Cα-bimodal peptide nucleic acids (bm-Cα-PNA) are PNAs with two faces and are designed homologues of PNAs in which each aminoethylglycine (aeg) repeating unit in the standard PNA backbone hosts a second nucleobase at Cα through a spacer chain with a triazole linker. Such bm-Cα-PNA with mixed sequences can form double duplexes by simultaneous binding to two complementary DNAs, one to the base sequence on t-amide side and the other to the bases on the Cα side chain. The synthesis of bm-Cα-PNA with homothymine (T7) on the t-amide face and homocytosine (C5) on the Cα side chain through the triazole linker was achieved by solid phase synthesis with the global click reaction. In the presence of complementary DNAs dA8 and dG6 at neutral pH, bm-Cα-PNA 1 forms a higher order pentameric double duplex of a triplex composed of two bm-Cα-PNA-C5:dG5 duplexes built on a core (bm-Cα-PNA-T7)2:dA8 triplex. Circular dichroism studies showed that assembly can be achieved by either triplex first and duplex later or vice versa. Isothermal titration calorimetry data indicated that the assembly is driven by favorable enthalpy. These results validate concurrent multiple complex formation by bimodal PNAs with additional nucleobases at Cα or Cγ on the aeg-PNA backbone and open up ways to design programmed supramolecular assemblies.

Cγ(S/R)-Bimodal Peptide Nucleic Acids (Cγ-bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands.

Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ(S)-bm-PNA duplexes are more stable than Cγ(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.

A conformation-specific IR spectroscopic signature for weak C[double bond, length as m-dash]OC[double bond, length as m-dash]O n→π* interaction in capped 4R-hydroxyproline.

Collagen, the most abundant protein in animals, has a unique triple helical structure comprising three parallel left-handed polyproline II (PPII) strands while each of the strands consists of a repeating sequence of X-Y-Gly, where X = proline (Pro) and Y = 4-hydroxyproline (Hyp). Collagen forms a stable triple helix of very long polypeptide strands despite the absence of intra-strand hydrogen bonding in the individual polypeptide chains. It has been reported that non-covalent n→π* interaction plays a significant role in stabilizing the individual polypeptide strands in collagen. However, there is no direct spectroscopic evidence for the presence of this interaction in collagen or its building block. Herein, we have observed for the first time a conformation-specific IR spectroscopic signature for C[double bond, length as m-dash]OC[double bond, length as m-dash]O n→π*-amide interaction in a capped Hyp residue, the most important monomer building block of collagen, using isolated gas phase IR spectroscopy and quantum chemistry calculations. The proof of the existence of this interaction in a model monomer has implications for better understanding of its role not only in structures of collagen but also most of the other proteins and larger peptides.

Stereodependent and solvent-specific formation of unusual ß-structure through side chain-backbone H-bonding in C4(S)-(NH2 /OH/NHCHO)-L-prolyl polypeptides.

It is shown that C4(S)-NH2 /OH/NHCHO-prolyl polypeptides exhibit PPII conformation in aqueous medium, but in a relatively hydrophobic solvent trifluoroethanol (TFE) transform into an unusual ß-structure. The stereospecific directing effect of H-bonding in defining the specific structure is demonstrated by the absence of ß-structure in the corresponding C4(S)-guanidinyl/(NH/O)-acetyl derivatives and retention of ß-structure in C4(S)-(NHCHO)-prolyl polypeptides in TFE. The distinct conformations are identified by the characteristic CD patterns and supported by Raman spectroscopic data. The solvent dependent conformational effects are interpreted in terms of intraresidue H-bonding that promotes PPII conformation in water, switching over to interchain H-bonding in TFE. The present observations add a new design principle to the growing repertoire of strategies for engineering peptide secondary structural motifs for innovative nanoassemblies and new biomaterials.

Fluorinated Peptide Nucleic Acids with Fluoroacetyl Side Chain Bearing 5-(F/CF3)-Uracil: Synthesis and Cell Uptake Studies.

Fluorine incorporation into organic molecules imparts favorable physicochemical properties such as lipophilicity, solubility and metabolic stability necessary for drug action. Toward such applications using peptide nucleic acids (PNA), we herein report the chemical synthesis of fluorinated PNA monomers and biophysical studies of derived PNA oligomers containing fluorine in in the acetyl side chain (-CHF-CO-) bearing nucleobase uracil (5-F/5-CF3-U). The crystal structures of fluorinated racemic PNA monomers reveal interesting base pairing of enantiomers and packing arrangements directed by the chiral F substituent. Reverse phase HPLC show higher hydrophobicity of fluorinated PNA oligomers, dependent on the number and site of the fluorine substitution: fluorine on carbon adjacent to the carbonyl group induces higher lipophilicity than fluorine on nucleobase or in the backbone. The PNA oligomers containing fluorinated bases form hybrids with cDNA/RNA with slightly lower stability compared to that of unmodified aeg PNA, perhaps due to electronic effects. The uptake of fluorinated homooligomeric PNAs by HeLa cells was as facile as that of nonfluorinated PNA. In conjunction with our previous work on PNAs fluorinated in backbone and at N-terminus, it is evident that the fluorinated PNAs have potential to emerge as a new class of PNA analogues for applications in functional inhibition of RNA.