Antiparallel (biochemistry) | EPFL Graph Search

In biochemistry, two biopolymers are antiparallel if they run parallel to each other but with opposite directionality (alignments). An example is the two complementary strands of a DNA double helix, which run in opposite directions alongside each other. Nucleic acids Nucleic acid molecules have a phosphoryl (5') end and a hydroxyl (3') end. This notation follows from organic chemistry nomenclature, and can be used to define the movement of enzymes such as DNA polymerases relative to the DNA strand in a non-arbitrary manner. G-quadruplexes G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures are normally located at the telomeres (the ends of the chromosomes). The G-quadruplex can either be parallel or antiparallel depending on the loop configuration, which is a component of the structure. If all the DNA strands run in the same direction, it is termed to be a parallel quadruplex, and is kno

Synthese und Paarungseigenschaften von pDNA und deren Anwendung bei der Entwicklung funktionalisierter Ribozyme

Damian Ackermann

Within this project methods for the preparation of the unnatural nucleic acids 3'-O-Methyl-pRNA and pDNA (3'-Desoxy-pRNA) were developed. The pairing properties of these two systems have been examined and compared with that of pRNA. All of the three systems do follow the same pairing rules. Pairing has been observed only on the Watson-Crick side forming duplexes in antiparallel direction. All three systems are autonomous pairing systems that do not interact with RNA or DNA. In this series pRNA forms the most stable duplexes. Nucleobase 9H-purin-2,6-diamin instead of adenin and 5-methyl-cytosine instead of cytosine were introduced to increase the stability of pDNA duplexes. A solution structure of the self-complementary pDNA sequence [MGAATTMG]2 was elucidated by NMR. It shows an antiparallel duplex twisted against the major groove with sligthly lefthanded helicity. In analogy to pRNA the interstrand stacking predominates with a inclination angel of approximately 45°. Proceeding form the NMR structure a MD simulation was performed, in which the duplex has strongly bent after a regeneration time of 1.5 ns; this bent shape was conserved during the remaining simulation time of 4.0 ns. Using automated solid phase synthesis pDNA/RNA hybrid sequences were prepared. Examining the pairing strength, the RNA-2'—>4'-pDNA linkage at the pDNA/RNA interface was observed to lead to more stable duplexes than the RNA-3'—>4'-pDNA linkage did. This kind of pDNA/RNA structures have been used to replace structure defining elements like hairpins or stem motifs by pDNA-duplexes in complex RNA structures. From the FMN binding RNA aptamer an analogous pDNA/RNA construct has been prepared, that was built of two hybrid sequences. The binding of FMN in the pDNA/RNA construct was shown by fluorescence spectroscopy and the dissociation constant K0 = 2.6·10-7 M was calculated. Using the same strategy a pDNA/RNA construct of the hammerhead ribozyme was prepared, having substrate cleavage activity in analogy to the natural ribozyme. Cleavage properties of the pDNA/RNA construct at different Mg2+ and Mn2+ concentrations and at different reaction temperatures showed the same trend as those from the natural ribozyme did. Under all measured conditions, the natural ribozyme was about 1.5 times as active as the pDNA/RNA construct. Additional functional groups were introduced at different positions of the pDNA/RNA hybrid sequences using a pre-functionalized 6'-bromopentyl allofuranosyl building bloc on which the bromide was substituted with MeNH2 resp. EtSH after solid phase synthesis. 25 different functionalized pDNA/RNA ribozyme constructs could be built up in a combinatorial way. From 17 out of the 25 constructs, the cleavage kinetics was measured and the cleavage rate evaluated. The substitution pattern of the most active pDNA/RNA ribozyme analogue was applied on the hammerhead RNA sequence and the doubly methylamino-substituted construct prepared. Compared to the natural hammerhead ribozyme, the cleavage rates of this construct were higher with a factor of 2.0 - 3.3 under all measured conditions.

EPFL2004

Synthesis and pairing properties of 3'-deoxyribopyranose (4' -> 2')-oligonucleotides ('p-DNA')

Damian Ackermann

The prepn. and the pairing properties of the new 3'-deoxyribopyranose (4'->2')-oligonucleotide (= p-DNA) pairing system, based on 3'-deoxy-b-D-ribo-pyranose nucleosides is presented. D-Xylose was efficiently converted to the prefunctionalized 3-deoxyribopyranose deriv. 4-O-[(tert-butyl)dimethylsilyl]-3-deoxy-D-ribo-pyranose 1,2-diacetate (obtained as a 4:1 mixt. of a- and b-D-anomers). From this sugar building block, the corresponding, appropriately protected thymine, guanine, 5-methylcytosine, and purine-2,6-diamine nucleoside phosphoramidites were prepd. in a minimal no. of steps. These building blocks were assembled on a DNA synthesizer, and the corresponding p-DNA oligonucleotides were obtained in good yields after a one-step deprotection under std. conditions, followed by HPLC purifn. Qual., p-DNA shows the same pairing behavior as p-RNA, forming antiparallel, exclusively Watson-Crick-paired duplexes that are much stronger than corresponding DNA duplexes. Duplex stabilities within the three related (i.e., based on ribo-pyranose nucleosides) oligonucleotide systems p-RNA, p-DNA, and 3'-O-Me-p-RNA were compared with each other. Intrinsically, p-RNA forms the strongest duplexes, followed by p-DNA, and 3'-O-Me-p-RNA. However, by introducing the nucleobases purine-2,6-diamine and 5-methylcytosine instead of adenine and cytosine, a substantial increase in stability of corresponding p-DNA duplexes was obsd. [on SciFinder (R)]

2002

Ferrimagnetism of the magnetoelectric compound Cu2OSeO3 probed by Se-77 NMR

Jean-Philippe Ansermet, Helmuth Berger, Frédéric Mila

We present a thorough Se-77 nuclear-magnetic-resonance (NMR) study of a single crystal of the magnetoelectric compound Cu2OSeO3. The temperature dependence of the local electronic moments extracted from the NMR data is fully consistent with a magnetic phase transition from the high-T paramagnetic phase to a low-T ferrimagnetic state with 3/4 of the Cu2+ ions aligned parallel and 1/4 aligned antiparallel to the applied field of 14.09 T. The transition to this 3up-1down magnetic state is not accompanied by any splitting of the NMR lines or any abrupt modification in their broadening, hence there is no observable reduction in the crystal symmetry from its high-T cubic P2(1)3 space group. These results are in agreement with high-resolution x-ray diffraction and magnetization data on powder samples reported previously by Bos et al. [Phys. Rev. B 78, 094416 (2008)]. We also develop a mean-field theory description of the problem based on a microscopic spin Hamiltonian with one antiferromagnetic (J(afm) similar or equal to 68 K) and one ferromagnetic (J(fm) similar or equal to -50 K) nearest-neighbor exchange interaction.

2010

Synthese und Paarungseigenschaften von pDNA und deren Anwendung bei der Entwicklung funktionalisierter Ribozyme

Damian Ackermann

EPFL2004