#Dna backbone code#

Protein-protein interactions play a critical role in numerous biological processes, and understanding the nature of each interaction is of central importance in biology and biotechnology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. Y.) from the Ministry of Education, Culture, Sports, Science and Technology, Japan. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This work was supported by a Grant-in-Aid for Scientific Research on Priority Areas (No. Received: JAccepted: NovemPublished: December 26, 2012Ĭopyright: © 2012 Nojima et al. Zhurkin VB, Lysov YP, Ivanov VI (1978) Different families of double-stranded conformations of DNA as revealed by computer calculations.Citation: Nojima T, Konno H, Kodera N, Seio K, Taguchi H, Yoshida M (2012) Nano-Scale Alignment of Proteins on a Flexible DNA Backbone. Wing R, Drew HR, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE (1980) Crystal structure analysis of a complete tum of B-DNA. Weiner S J, Kollman PA, Nguyen DT, Case DA (1986) An all atom force field for simulations of proteins and nucleic acids. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta SJ, Weiner P (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. Srinivasan AR, Olson WK (1987) Nucleic acid model building: The multiple backbone solutions associated with a given base morphology. Sklenar H, Larvery R, Pullman B (1986) The flexibility of nucleic acids: (I) “SIR”, a novel approach to the vaariation of polymer geometry in constrained systems. The crystal and molecular structure of sodium adenylyn-3′, 5′-uridine hexahydrate. Seeman NC, Rosenberg JM, Park KJJ, Rich A (1976) RNA double-helical fragments at atomic resolution: I. Saenger W (1984) Principles of Nucleic Acid Structure. Paine GH, Scheraga HA (1985) Prediction of the native conformation of a polypeptide by statistical mechanical procedure: I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix. Miller KJ (1979) Interactions of molecules with nucleic acids.

Metropolis N, Rosenbluth AW, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines.

#Dna backbone code#

Matthews BW (1988) No code for recognition. Marky LA, Breslauer KJ (1987) Origins of netropsin binding affiniy and specificity: correlations of thermodynamic and structural data.

Hansen JP, McDonald IR (1986) Theory of Simple Liquids. García AE, Krumhansl JA (1987) Agreement between single crystal X-ray and molecular mechanical supar ring conformations. Pseudorotatoin in saturated five-membered ring compounds. Proc Natl Acad Sci USA 84: 8385–8389Ĭremer D, Pople JA (1975) Molecular orbital theory of the electronic structure of organic compounds. Oxford University Press New YorkĬoll M, Federick CA, Wang AH-J, Rich A (1987) A bifurcated hydrogen-bonded conformation in the d(AOT) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Springer-Verlag New YorkĬhandler D (1987) Introduction to Modern Statistical Mechanics. CRC Boca Raton FL.īinder K (ed) (1979) Monte Carlo Methods in Statistical Physics. J Am Chem Soc 94: 8205–8212Īrnott S, Campbell-Smith P, Chandrasekaran P (1979) CRC Handbook of Biochemistry, Vol. A new description using the concept of pseudorotation. Clarendon Press OxfordĪltona C, Sundaralingam M (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. This process is experimental and the keywords may be updated as the learning algorithm improves.Īllen MP, Tildesley DJ (1987) Computer Simulation of Liquids. These keywords were added by machine and not by the authors. In order to understand its role in the recognition process, it is necessary to have a simple yet rigorous method to model DNA backbone structure. The narrower minor groove in the central (AT) n segments of the dodecamers d(CGCGAATTCGCG) 2 and d(CGCAAATTTGCG) 2 help to stabilize the interaction between DNA and minor groove binding drugs (e.g., netropsin, distamycin, etc.) (Federick et al., 1987). For example, the recognition mechanism for the trp repressor molecule to the operator sequence is attrubuted to the backbone structure of the DNA molecule (Matthews, 1988). In recent years, experimental data has indicated that the sugar-phosphate backbone can play an important role in the recognition of DNA by protein or drug molecules (Marky and Breslauer, 1987 Matthews, 1988 Federick et al., 1987).