Biophysics of Recombination Bibliography

* Indicates listing on more than one bibliography.

*N.C. Seeman, Nucleic Acid Junctions: Building Blocks for Genetic Engineering in Three Dimensions. In: Biomolecular Stereodynamics, ed. by R.H. Sarma, Adenine Press, New York (1981), pp. 269-277.

N.C. Seeman and B.H. Robinson, Simulation of Double Stranded Branch Point Migration. In: Biomolecular Stereodynamics, ed by R.H. Sarma, Adenine Press, New York (1981), pp. 279-300.

*N.C. Seeman, Nucleic Acid Junctions and Lattices. Journal of Theoretical Biology 99, 237-247 (1982).

*N.C. Seeman and N.R. Kallenbach, Design of Immobile Nucleic Acid Junctions. Biophysical Journal 44, 201-209 (1983).

*N.C. Seeman and N.R. Kallenbach, Nucleic Acid Junctions, The Tensors of Life? In: Nucleic Acids: The Vectors of Life, ed. by B. Pullman and J. Jortner, D. Reidel, Dordrecht, 183-200 (1983).

*N.R. Kallenbach, R.-I. Ma and N.C. Seeman, An Immobile Nucleic Acid Junction Constructed from Oligonucleotides. Nature 305, 829-831 (1983).

N.R. Kallenbach, R.-I. Ma, A.J. Wand, G.H. Veeneman, J.H. van Boom and N.C. Seeman, Fourth Rank Immobile Nucleic Acid Junctions. Journal of Biomolecular Structure and Dynamics 1, 158-168 (1983).

N.C. Seeman, M.F. Maestre, R.-I. Ma and N.R. Kallenbach, Physical Characterization of a Nucleic Acid Junction. In: Progress in Clinical and Biological Research, Vol. 172A: The Molecular Basis of Cancer, ed. by R. Rein, Alan R. Liss Inc., New York (1985), pp. 99-108.

D.E. Wemmer, A.J. Wand, N.C. Seeman and N.R. Kallenbach, NMR Analysis of DNA Junctions: Imino Proton NMR Studies of Individual Arms and Intact Junction. Biochemistry 24, 5745-5749 (1985).

N.R. Kallenbach and N.C. Seeman, Stable Branched DNA Structures: DNA Junctions. Comments on Cellular and Molecular Biophysics 4, 1-16 (1986).

B.H. Robinson and N.C. Seeman, The Kinetics of Double Stranded Branch Point Migration. Biophysical Journal 51, 611-626 (1987).

L.A. Marky, N.R. Kallenbach, K.A. McDonough, N.C. Seeman and K.J. Breslauer, The Melting Behavior of a Nucleic Acid Junction: A Calorimetric and Spectroscopic Study. Biopolymers 26, 1621-1634 (1987).

*N.C. Seeman and N.R. Kallenbach, Nucleic Acid Junctions: A Successful Experiment in Macromolecular Design. In: Molecular Structure: Chemical Reactivity and Biological Activity, ed. by J.J. Stezowski J.-L. Huang and M.-C. Shao, Oxford University Press, Oxford, (1988) pp. 189-194.

M.E.A. Churchill, T.D. Tullius, N.R. Kallenbach and N.C. Seeman, A Holliday Recombination Intermediate is Twofold Symmetric. Proceedings of the National Academy of Sciences (USA) 85, 4653-4656 (1988).

M.L. Petrillo, C.J. Newton, R.P. Cunningham, R.-I. Ma, N.R. Kallenbach and N.C. Seeman. The Ligation and Flexibility of 4-Arm DNA Junctions. Biopolymers, 27, 1337-1352 (1988).

J.-H. Chen, M.E.A. Churchill, T.D. Tullius, N.R. Kallenbach and N.C. Seeman, Construction and Analysis of Mono-Mobile DNA Junctions. Biochemistry 27, 6032-6038 (1988).

J.E. Mueller, B. Kemper , R.P. Cunningham, N.R. Kallenbach and N.C. Seeman, T4 Endonuclease VII Cleaves the Crossover Strands of Holliday Junction Analogs. Proceedings of the National Academy of Sciences (U.S.A.) 85, 9441-9445 (1988).

N.C. Seeman, J.-H. Chen and N.R. Kallenbach, Gel Electrophoretic Analysis of DNA Branched Junctions Electrophoresis 10, 345-354 (1989).

Q. Guo, N.C. Seeman and N.R. Kallenbach, Site-Specific Interaction of Intercalating Drugs with a Branched DNA Molecule. Biochemistry 28, 2355-2359 (1989).

M. Lu, Q. Guo, N.C. Seeman and N.R. Kallenbach, DNase I Cleavage of Branched DNA Molecules, Journal of Biological Chemistry 264, 20851-20854 (1989).

F. Jensch, H. Kosak, N.C. Seeman and B. Kemper , Cruciform Cutting Endonucleases From S. cerevisiae and Phage T4 Show Conserved Reactions With Branched DNAs, EMBO Journal, 8, 4325-4334 (1989).

N.C. Seeman, J.E. Mueller, J.-H. Chen, M.E.A. Churchill, A. Kimball, T.D. Tullius, B. Kemper , R.P. Cunningham and N.R. Kallenbach, Immobile Junctions Suggest New Features of the Structural Chemistry of Recombination, In: Structure & Methods: Human Genome Initiative & DNA Recombination, Vol 1, R.H. Sarma and M.H. Sarma, eds., Adenine Press, New York, pp. 137-156 (1990).

Q. Guo, M. Lu, N.C. Seeman and N.R. Kallenbach, Drug Binding by Branched DNA Molecules: Analysis by Chemical Footprinting of Intercalation into an Immobile Junction,Biochemistry 29, 570-578, (1990).

M. Lu, Q. Guo, R.F. Pasternack, D.J. Wink. N.C. Seeman and N.R. Kallenbach, Drug Binding by Branched DNA: Selective Interaction of Tetrapyridyl Porphyrins with an Immobile Junction, Biochemistry 29, 1614-1624 (1990).

A. Kimball, Q. Guo, M. Lu, N.R. Kallenbach, R.P. Cunningham, N.C. Seeman and T.D. Tullius, Conformational Isomers of Holliday Junctions, Journal of Biological Chemistry 265, 6544-6547 (1990).

M. Lu, Q. Guo, N.C. Seeman and N.R. Kallenbach, Drug Binding by Branched DNA: Selective Interaction of the Dye Stains-All with an Immobile Junction, Biochemistry 29, 3407-3412 (1990).

J.E. Mueller, C.J. Newton, F. Jensch, B. Kemper , R.P. Cunningham, N.R. Kallenbach and N.C. Seeman, Resolution of Holliday Junction Analogs by T4 Endonuclease VII Can Be Directed By Substrate Structure, Journal of Biological Chemistry 265, 13918-13924 (1990).

M. Lu, Q. Guo, J.E. Mueller, B. Kemper , F.W. Studier, N.C. Seeman and N.R. Kallenbach, Characterization of a Bimobile DNA Junction, Journal of Biological Chemistry 265, 16778-16785 (1990).

*Y. Wang, J.E. Mueller, B. Kemper , and N.C. Seeman, The Assembly and Characterization of 5-Arm and 6-Arm DNA Junctions, Biochemistry 30, 5667-5674 (1991).

M. Lu, Q. Guo, N.C. Seeman and N.R. Kallenbach, Parallel and Antiparallel Holliday Junctions Differ in Structure and Stability, Journal of Molecular Biology 221, 1419-1432 (1991).

M. Lu, Q. Guo, L.A. Marky, N.C. Seeman and N.R. Kallenbach, Thermodynamics of DNA Chain Branching Journal of Molecular Biology 223, 781-789 (1992).

*S.M. Du, S. Zhang and N.C. Seeman, DNA Junctions, Antijunctions and Mesojunctions, Biochemistry 31, 10955-10963 (1992).

T.-J. Fu and N.C. Seeman, DNA Double Crossover Structures, Biochemistry 32, 3211-3220 (1993).

S. Zhang, T.-J. Fu and N.C. Seeman, Construction of Symmetric, Immobile DNA Branched Junctions, Biochemistry 32, 8062-8067 (1993).

*N.C. Seeman and N.R. Kallenbach, DNA Branched Junctions, Annual Review of Biophysics and Biomolecular Structure 23, 53-86 (1994).

*T-J. Fu, Y.-C. Tse-Dinh, and N.C. Seeman, Holliday Junction Crossover Topology, Journal of Molecular Biology 236, 91-105 (1994).

T.-J. Fu, B. Kemper and N.C. Seeman, Endonuclease VII Cleavage of DNA Double Crossover Molecules, Biochemistry 33, 3896-3905 (1994).

S. Zhang, and N.C. Seeman, Symmetric Holliday Junction Crossover Isomers, Journal of Molecular Biology 238, 658-668 (1994).

D.M.J. Lilley, R.M. Clegg, S. Diekmann, N.C. Seeman, E. von Kitzing and P. Hagerman, A Nomenclature of Junctions and Branchpoints in Nucleic Acids, European Journal of Biochemistry 230, 1-2 (1995).

*J.A. Sekiguchi, N.C. Seeman and S. Shuman, Asymmetric Resolution of Holliday Junctions by Eukaryotic DNA Topoisomerase I. Proceedings of the National Academy of Sciences (USA) 93, 785-789 (1996).

*H. Qiu, J.C. Dewan and N.C. Seeman, A DNA Decamer with a Sticky End: The Crystal Structure of d-CGACGATCGT. J. Mol. Biol. 267, 881-898 (1997).

X. Li, H. Wang and N.C. Seeman, Direct Evidence for Holliday Junction Crossover Isomerization. Biochemistry 36, 4240-4247 (1997).

W. Sun, C. Mao, F. Liu and N.C. Seeman, Sequence Dependence of Branch Migratory Minima. J. Mol. Biol. 282, 59-70 (1998).

*R. Sha, F. Liu, M. Bruist and N.C. Seeman, Parallel Helical Domains in DNA Branched Junctions Containing 5', 5' and 3', 3' Linkages, Biochemistry 38, 2832-2841 (1999).

*C. Mao, W. Sun and N.C. Seeman, Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy, Journal of the American Chemical Society 121, 5437-5443 (1999).

*W. Sun, C. Mao, H. Iwasaki, B. Kemper and N.C. Seeman, No Braiding of Holliday Junctions in Positively Supercoiled DNA Molecules, Journal of Molecular Biology 294, 683-699 (1999).

R. Sha, F. Liu and N.C. Seeman, Direct Evidence for Spontaneous Branch Migration in Antiparallel DNA Holliday Junctions, Biochemistry 39, 11514-11522 (2000).

R. Sha, H. Iwasaki, F. Liu, H. Shinagawa and N.C. Seeman, Cleavage of Symmetric Immobile DNA Junctions by Ruv C, Biochemistry 39, 11982-11988 (2000).

*R. Sha, F. Liu, D.P. Millar N.C. Seeman, Atomic Force Microscopy of Parallel DNA Branched Junction Arrays, Chemistry & Biology 7, 743-751 (2000).

*A. Podtelezhnikov, C. Mao, N.C. Seeman & A. Vologodskii, Multimerization-Cyclization of DNA Fragments as a Method of Conformational Analysis, Biophys. J. 79, 2692-2704 (2000).

*R. Sha, F. Liu and N.C. Seeman, Atomic Force Measurement of the Interdomain Angle in Symmetric Holliday Junctions, Biochemistry 41, 5950-5955 (2002).

R. Sha, F. Liu, H. Iwasaki and N.C. Seeman, Parallel Symmetric Immobile DNA Junctions as Substrates for E. coli RuvC Holliday Junction Resolvase. Biochemistry 41, 10985-10993 (2002).

S. Liao, C. Mao, J.J. Birktoft, S. Shuman and N.C. Seeman, Resolution of Undistorted Symmetric Immobile DNA Junctions by Vaccinia Topoisomerase I, Biochemistry 43, 1520-31 (2004).

*X. Wang & N.C. Seeman, The Assembly and Characterization of 8-Arm and 12-Arm DNA Branched Junctions, J. Am. Chem. Soc., 129, 8169-8176 (2007).

*C. Lin, S. Rinker, X. Wang, Y. Liu, N. C. Seeman & H. Yan, In Vivo Cloning of Artificial  DNA Nanostructures, Proc. Nat. Acad. Sci. (USA) 105, 17626-17631 (2008).

*C.H. Spink, L. Ding, Q. Yang, R.D. Sheardy & N.C. Seeman, Thermodynamics of Forming a Parallel Holliday Crossover, Biophys. J. 97, 528-538 (2009).

*J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha, P.E. Constantinou, S.L. Ginell, C. Mao, & N.C. Seeman, From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal, Nature 461, 74-77 (2009).

* H. Gu, W. Yang & N.C. Seeman, A DNA Scissors Device Used to Measure MutS Binding to DNA Mis-Pairs, J. Am. Chem. Soc. 132, 4352-4357 (2010).

* X. Wang, X. Zhang, C. Mao & N.C. Seeman, Double-Stranded DNA Homology Produces a Physical Signature, Proc. Nat. Acad. Sci. (USA) 107,  12547-12552 (2010).

* M.I. Lvovska, N.C. Seeman, R. Sha, T.R. Globus, T.B. Khromova & T.S. Dorofeeva, THz Characterization of DNA Four-Way Junctions and its Components, IEEE Trans. Nanotech. 9, 610-617 (2010).

* H.K.K. Subramanian, B. Chakraborty, R. Sha & N.C. Seeman, The Label-Free Unambiguous Detection and Symbolic Display of Single Nucleotide Polymorphisms on DNA Origami, NanoLett. 11, 910-913 (2011).

* T. Wang, R. Sha, R. Dreyfus, M.E. Leunissen, C. Maass, D. Pine, P.M. Chaikin & N.C. Seeman, Self-Replication of Information-Bearing Nanoscale Patterns, Nature, 478, 225-228 (2011).

* C. Liu, E. Kim, B. Demple & N.C. Seeman, A DNA-Based Nanomechanical Device Used to Characterize the Distortion of DNA by Apo-SoxR Protein, Biochem. 51, 937-943 (2012).

* M. Ye, J. Guillaume, Y. Liu, R. Sha, R. Wang, N.C. Seeman & J.W. Canary, Site-Specific Inter-Strand Cross-Links of DNA Duplexes, Chem. Sci. 4, 1319-1329 (2013).

 

Return to Seeman Lab Recombination Intermediates Page

Go to Homepage for Ned Seeman's Lab