Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
The results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics.
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two DNA quadruplex (G-DNA) molecules, namely the antiparallel d(G4T4G4)2 dimeric quadruplex with diagonal loops…
Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.
For the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats is shown and improved thermodynamic parameters allow to predict much more accurately the thermodynamics stabilities and structures of CNG RNAs.
The Apical Loop of the HIV-1 TAR RNA Hairpin Is Stabilized by a Cross-loop Base Pair*
- T. Kulinski, M. Olejniczak, R. Adamiak
- Biology, ChemistryJournal of Biological Chemistry
- 3 October 2003
The TAR hairpin of the HIV-1 RNA genome is indispensable for trans-activation of the viral promoter and virus replication. The TAR structure has been studied extensively, but most attention has been…
Conformational analysis of galanin using end to end distance distribution observed by Förster resonance energy transfer
The coexistence of different structures of the neuropeptide galanin in trifluoroethanol solution was revealed by the model independent analysis of the distribution of relaxation times from the time-resolved resonance energy transfer data.
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
Spatial Distribution Functions As a Tool in the Analysis of Ribonucleic Acids Hydration - Molecular Dynamics Studies
Watson–Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation
- W. Rypniewski, K. Banaszak, T. Kulinski, A. Kiliszek
- ChemistryRNA: A publication of the RNA Society
- 1 January 2016
Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing.
Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA
Spectroscopic investigations of the single tryptophan residue and of riboflavin and 7-oxolumazine bound to lumazine apoprotein from Photobacterium leiognathi.
A new method is designed for evaluation of the rate constant of energy transfer by measuring the (picosecond) rise time of the acceptor fluorescence, which indicates no change in secondary structure on binding to the apoprotein.