RESUMO
Structure and dynamics of an undecamer DNA duplex containing a single alpha-anomeric deoxyadenosine residue placed in opposition to a thymidine unit have been studied using simulation of molecular dynamics in aqueous solution. Despite several noticeable deviations from the B-DNA duplex structure caused by the anomerisation, such as: West type puckering of the alpha-anomeric sugar, disrupted base stacking pattern and unstable duplex bending, the formation of a non-classical alpha-dA-T pair was observed. A novel way of visual presentation of trajectory data allowing high throughput screening of the conformational parameters is presented.
Assuntos
DNA/química , Desoxiadenosinas/química , Ácidos Nucleicos Heteroduplexes/química , Sequência de Bases , Modelos Moleculares , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Fatores de TempoRESUMO
Structure and dynamics of adenosine loops in RNA bulge duplexes was studied using time-resolved spectrofluorimetry and in aqua simulation of molecular dynamics. Thermodynamics revealed that 2-aminopurine riboside is an non-invasive fluorescent probe when built within the bulge region of chemically synthesized RNA duplexes.
Assuntos
2-Aminopurina , Adenosina/química , Corantes Fluorescentes , RNA/química , 2-Aminopurina/química , Sequência de Bases , Simulação por Computador , Corantes Fluorescentes/química , Conformação de Ácido Nucleico , RNA de Cadeia Dupla/síntese química , RNA de Cadeia Dupla/química , Espectrometria de Fluorescência , Termodinâmica , Fatores de TempoRESUMO
Structural properties of the fluorescent alpha-anomeric 1,N(6)ethenodeoxyadenosine residue placed in opposition to all four canonical deoxynucleotide units within 11-mer DNA duplexes have been studied. The duplex with alpha-epsilondA / dG pairing is most thermodynamically stable while the alpha-epsilondA / dC one is the least stable. Fluorescence measurements confirm the thermodynamic data and indicate base-pair dependent stacking properties of alpha-epsilondA within duplex structures. Results of molecular dynamics (MD) simulations in aqueous solution for the most stable duplex point to the presence of different conformational states of the alpha-1,N(6)etheno-deoxyadenosine residue, including formation of a hydrogen bonded pair with the dG and possible occurrence of severe kinking in the duplex.
Assuntos
DNA/química , Desoxiadenosinas/química , Sequência de Bases , Fluorescência , Espectrofotometria Ultravioleta , TermodinâmicaRESUMO
5-Fluorouridine residues have been introduced into functionally important bulge and loop regions of 29-mer HIV-1 TAR RNA hairpins I and II to study Mg2+ and Ca2+ binding using 19F-NMR spectroscopy. There was no substantial binding detected up to 20-molar excess in case of both cations, whereas association of argininamide, used as a reference ligand, could be detected at less than 1-molar excess. The deltadelta 19F value of 1.93 ppm observed for (F)U23 upon argininamide binding is in agreement with former NMR studies of TAR RNA/argininamide complex. However, obtained results do not confirm U38 x A27 x U23 base-triple formation. The unmodified HIV-1 TAR RNA hairpin resulted from 600 ps in aqua molecular dynamics simulation was subjected to a molecular mechanics modelling of Mg+ binding.
