Electronic Structures and Spectra of the Bases and Base Pairs of Nucleic Acids

The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transition energies of low-lying excited states and discuss the band characters. The results indicate that the calculated spectra are in good agreement with experimental values. On the other hand, our calculations for A-T and G-C pairs are very beneficial to understanding hydrogen bond properties of these pairs.

Cis Watson-Crick/Watson-Crick Base Pairs in DNA： A Density Functional Theory(DFT) Study

The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^（＊＊） basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis（NBO） was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick（WC） edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

Stabilization and Multiple-Responsive Recognition of Natural Base Pairs in Water by a Cationic Cage

The hydrogen-bonded(H-bonded)base pairs,double H-bonded A•T and triple H-bonded G•C in DNA,are important units for storing,encoding,and expressing genetic information.Owing to the interference from water,however,the formation of H-bonded base pairs from short deoxynucleotide fragments such as mono-or di-deoxynucleotide are not easily achieved in aqueous solutions.

Pt(Ⅱ), Pd(Ⅱ) and Ni(Ⅱ) Complexes Binding to the N(7) Position of Guanine: Influence on the Guanine and Watson-crick GC Base Pair

Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.

Preparation of bowl-shaped polydopamine surface imprinted polymer composite adsorbent for specific separation of 2'-deoxyadenosine

Molecularly imprinted polymers (MIPs) have great potential as adsorbents for selective adsorption and separation of nucleoside compounds,but effectively enhancing the affinity of recognition sites by adjusting the forces between template molecules and functional monomers remains an important challenge.In this work,a surface imprinting strategy was used to construct bowl-shaped molecularly imprinted composite sorbents (BHPN@MIPs) based on polydopamine (PDA) particles and have achieved selective separation and purification of 2'-deoxyadenosine (dA).Where by the base complementary pairing interaction of the combined template molecule d A and the pyrimidine functional monomer can enhance the preassembly force,and the hydrophilic bowl-shaped PDA can provide a larger storage space contact efficiency of d A in the test solution,causing the site utilization much higher and improving the kinetic adsorption performance.The equilibrium adsorption time and maximum adsorption capacity of60 min and 328.45μmol·g^(-1)were observed by static adsorption experiments,and the selectivity experimental results showed an imprinting factor IF of 1.30.After four adsorption–desorption cycles,the initial adsorption equilibrium adsorption capacity of BHPN@MIPs still retained 91.14%.By evaluating the selective adsorption of d A in spiked human serum solutions,BHPN@MIPs can be used to selectively enrich and analyze target d A in complex biological samples.

Compact on-chip 1×2 wavelength selective switch based on silicon microring resonator with nested pairs of subrings

We propose and experimentally demonstrate compact on-chip 1×2 wavelength selective switches(WSSs) based on silicon microring resonators(MRRs) with nested pairs of subrings(NPSs). Owing to the resonance splitting induced by the inner NPSs, the proposed devices are capable of performing selective channel routing at certain resonance wavelengths of the outer MRRs. System demonstration of dynamic channel routing using fabricated devices with one and two NPSs is carried out for 10 Gb∕s non-return-to-zero signal. The experimental results verify the effectiveness of the fabricated devices as compact on-chip WSSs.

Parallel DNA Constrained by“CC^+Clamps”

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Molecular recognition and homochirality preservation of guanine tetrads in the presence of melamine

Molecular recognition between nucleobases plays a crucial role in all kinds of biological processes.However,real-space investigation of the recognition capability of nucleobases in the presence of interfering compounds remains unexplored.Herein,based on the combination of scanning tunneling microscopy imaging and density functional theory modeling,we report the impact of the presence of melamine(M)on the formation and chirality of guanine(G)-tetrads on Au(111).Although M can interact with G by double hydrogen bonding,the Hoogsteen base pairing of G is not compromised,forming identical individual G-tetrads as would have happened without the presence of M.G-tetrads coexist with M on the surface not only in separate domains,but also within the mixture network of G-tetrads and M-dimers.Although the adsorption orientation of G-tetrads in the mixture network diversifies into two distinct angles,all G-tetrads in the network keep the same chirality,emphasizing the high preference of homochirality in such biochemical systems.