Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids

Some selected amino acids, in particular l-aspartic acid (l-Asp) and l-histidine (l-His), can function as leaving group during polymerase-catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. Although l-Asp-dAMP and l-His-dAMP bind, most probably, in a different way in the active site of the enzyme, aspartic acid and histidine can be considered as mimics of the pyrophosphate moiety of deoxyadenosine triphosphate. l-Aspartic acid is more efficient than d-aspartic acid as leaving group. Such P-N conjugates of amino acids and deoxynucleotides provide a novel experimental ground for diversifying nucleic acid metabolism in the field of synthetic biology

Galactosylsphingamides : new α-GalCer analogues to probe the F’-pocket of CD1d

Invariant Natural Killer T-cells (iNKT-cells) are an attractive target for immune response modulation, as upon CD1d-mediated stimulation with KRN7000, a synthetic alpha-galactosylceramide, they produce a vast amount of cytokines. Here we present a synthesis that allows swift modification of the phytosphingosine side chain by amidation of an advanced methyl ester precursor. The resulting KRN7000 derivatives, termed alpha-galactosylsphingamides, were evaluated for their capacity to stimulate iNKT-cells. While introduction of the amide-motif in the phytosphingosine chain is tolerated for CD1d binding and TCR recognition, the studied alpha-galactosylsphingamides showed compromised antigenic properties

Molecular-dynamics studies of single-stranded hexitol, altritol, mannitol, and ribose nucleic acids (HNA, MNA, ANA, and RNA, resp.) and of the stability of HNA·RNA, ANA·RNA, and MNA·RNA duplexes

The influence of the orientation of a 3'-OH group on the conformation and stability of hexitol oligonucleotides in complexes with RNA and as single strands in aqueous solution was investigated by molecular-dynamics (MD) simulations with AMBER 4.1. The particle mesh Ewald (PME) method was used for the treatment of long-range electrostatic interactions. An equatorial orientation of the 3'-OH group in the single-stranded D-mannitol nucleic acid (MNA) m(GCGTAGCG) and in the complex with the RNA r(CGCAUCGC) has an unfavorable influence on the helical stability. Frequent H-bonds between the 3'-OH group and the O-C(6') of the phosphate backbone of the following nucleotide explain the distorted conformation of the MNA·RNA complex as well as that of the single MNA strand. This is consistent with experimental results that show lowered hybridization potentials for MNA·RNA complexes. An axial orientation of the 3'-OH group in the D-altritol nucleic acid (ANA) a(GCGTAGCG) leads to a stable complex with the complementary RNA r(CGCAUCGC), as well as to a more highly preorganized single-stranded ANA chain. The averaged conformation of the ANA·RNA complex is similar to that of A-RNA, with only minor changes in groove width, helical curvature, and H-bonding pattern. The relative stabilities of ANA·RNA vs. HNA·RNA (HNA = D-hexitol nucleic acid without 3'-OH group) can be explained by differences in restricted movements, H-bonds, and solvation effects

Poly(2-acrylamido-2-methyl-1-propanamide) (PAMPA): A neutral, water-soluble synthetic polymer with double-stranded helix conformation

A new synthetic polymer, poly(2-acrylamido-2-methyl-1-propanamide) (PAMPA), is described. It combines the structural features of poly(leucine) and poly(glutamine), its molecular weight averages 42000 D, and it contains ca. 270 residues. A 13C-NMR-tacticity study indicates that it consists of a mixture of syndiotactic (38%), heterotactic (48%), and isotactic (17%) polymer. PAMPA has a tendency to self-organize into a coiled-coil double-stranded helix structure in aqueous solution, as determined by Fourier-transform infrared spectroscopy (FT-IR). Molecular modeling of PAMPA shows that the helix formation is driven by repeated intramolecular H-bonds between nearest-neighbor amide groups, and that the structure is further stabilized by hydrophobic interactions between the two lateral Me groups. PAMPA has a neutral structure, is highly water-soluble, and demonstrates temperature stability

From M-tuberculosis thymidine monophosphate kinase (TMPKmt) inhibitors towards mitochondrial thymidine kinase (TK-2) inhibitors

Here, we report on the enzyme structure-aided design of a series of substituted 3'- or 5'-thiourea derivatives of beta- and alpha-thymidine, respectively, as thymidine monophosphate kinase inhibitors of M. tuberculosis. In a recent study, several 3'-thiourea substituted thymidine derivatives were found to be exquisitely potent and specific inhibitors of mitochondrial thymidine kinase (TK-2), with high selectivity when compared with cytosolic TK-1