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 calculati...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.展开更多
Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices...Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.展开更多
Watson Crick automata are finite automata working on double strands. Extensive research work has already been done on non deterministic Watson Crick automata and on deterministic Watson Crick automata. Parallel Commun...Watson Crick automata are finite automata working on double strands. Extensive research work has already been done on non deterministic Watson Crick automata and on deterministic Watson Crick automata. Parallel Communicating Watson Crick automata systems have been introduced by E. Czeziler et al. In this paper we discuss about a variant of Watson Crick automata known as the two-way Watson Crick automata which are more powerful than non-deterministic Watson Crick automata. We also establish the equivalence of different subclasses of two-way Watson crick automata. We further show that recursively enumerable (RE) languages can be realized by an image of generalized sequential machine (gsm) mapping of two-way Watson-Crick automata.展开更多
基金Project supported by the National Key Research and Development Project(No.2016YFB0201404)
文摘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.
文摘Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.
文摘Watson Crick automata are finite automata working on double strands. Extensive research work has already been done on non deterministic Watson Crick automata and on deterministic Watson Crick automata. Parallel Communicating Watson Crick automata systems have been introduced by E. Czeziler et al. In this paper we discuss about a variant of Watson Crick automata known as the two-way Watson Crick automata which are more powerful than non-deterministic Watson Crick automata. We also establish the equivalence of different subclasses of two-way Watson crick automata. We further show that recursively enumerable (RE) languages can be realized by an image of generalized sequential machine (gsm) mapping of two-way Watson-Crick automata.
