Linjing Yang

Molecular structures of recognition system host + guest and DNA complex

Abstract Investigations were carried out to look into the system of host + guest as a ligand targeted to the duplex DNA. The possible structures of host RhB-β-CDen were studied by minimization and molecular dynamics simulation. In the association state of host + guest (1:1) system, the guest molecule of 1-borneol could insert into the cyclodextrin cavity of the host molecule RhB-β-CDen. The interactive sites of the RhB-β-CDen + borneol system as a ligand targeting to the duplex DNA d(C)8·d(G)8 were obtained by docking interaction. It was found that the ligand was probably bound to the duplex DNA in the minor groove. The conformations of DNA varies noticeably to accommodate the binding groups of the ligand. Water molecules bridge between the bases of duplex DNA and/or ligand by hydrogen bonds to make the entire system more stable.

Theoretical studies on conformation comparison of braid-like and triplex DNA

Abstract Based on the experimental data of scanning tunneling microscopy (STM), models of three-stranded braid-like DNAs composed by three kinds of base triplets AAA, TAT and GCA were constructed. We investigated the braid-like DNAs and their comparative triplex DNAs using a molecular mechanics method. The three strands of braid-like DNAs are proven equivalent, while those of triplex DNAs are not. The conformational energies for braid-like DNAs were found to be higher than that for triplex DNAs. Each period in one strand of braid-like DNA has 18 nucleotides, half of which are right-handed, while the other half are left-handed. Additional discussions concerning sugar puckering modes and the H-bonds are also included.

Influence of loop sequence on relative stability of bimolecular triplex DNA

The structures of 20 bimolecular triplexes have been built and simuleted by molecular mechanics. The sequence of pyrimidine strand is 5’-dTTCTTTC-L1 TTTI-3CTTTTcTT-3, where the five nucleotides underlined cornpaw Ioop sequences. L1 and L5 represent varied residues. The sequences of purine strands are 5′-dGAAAAGAA-3′ and the reversed orientation 5′-dAAGAAAG-3′. The influence of different loop sequences and compositicm on the relative stability of twenty triplexes have bem energetically analyzed. The results indicate that 5′-loop triplexes are more stable than 3′-loop ones and the stacking interaction of purines with their adjacent basw are stronger than that of pyrimidines. The stability of triplexes is mainly determined by the first and last nucleotides in the loop.

Loop and water effect on stability of intertriplex DNA

Abstract Stability of four intratriplexes and one intertriplex influenced by loops and water have been investigated by molecular mechanics calculation. The four intratriplexes are 5′-d(TC) 6 -d(T) m -d(CT) 6 -d(C) n -d(AG) 6 -3′ ( m , n = 3 or 4), the corresponding intertriplex is d(TC) 6 ∗d(AG) 6 ·d(CT) 6 (·, Watson-Crick hydrogen bond; ∗, Hoogsteen hydrogen bond). We studied in detail how loops and water would effect intra- and interstrand interactions of the five triplexes, respectively. The results showed that the existence of loops may have limited impact on the stability of the concerned triplex structures, regardless of water environment. In contrast, water molecules do have appreciable effects on triplex stability. Sugar conformations of the five triplexes were also discussed in this paper. The theoretical results are in good agreement with the FT-IR experiments.

Structural Studies on Host + Guest Recognition Sensory Systems

Rhodamine B-ethylenediamine-β-cyclodextrins (RhB-β-CDen) and rhodamine B-β-cyclodextrins (RhB-β-CD) can form inclusive complexes with many guest molecules, a reaction which can be used as a nucleic acid probe. In this paper, the most stable conformations of RhB-β-CDen and RhB-β-CD have been determined by fluorescence experiments and analyzed by molecular modeling simulation. The interaction between RhB-β-CDen and two guest molecules, 1-borneol and cyclohexanol, has also been investigated. The results showed that RhB-β-CDen has a stronger interaction with 1-borneol than with cyclohexanol. Borneol could push the three aromatic-rings of rhodamine B out of the CD cavity, while the cyclohexanol could not. The interactive sites of host and guest are also presented.