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2
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-
0022144562
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Gene synthesis machines
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Caruthers MH. Gene synthesis machines. Science. 230:1985;281-285.
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(1985)
Science
, vol.230
, pp. 281-285
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-
Caruthers, M.H.1
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3
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0002792997
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Molecular craftwork with DNA
-
of special interest. The goal of nanotechnology is to fashion structures on the nanometer scale with the same level of surety and control with which this can be done on the macroscopic scale. This article describes progress in using DNA as the medium for nanoconstruction.
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of special interest Seeman NC. Molecular craftwork with DNA. Chem Intelligencer. 1:1995;38-47 The goal of nanotechnology is to fashion structures on the nanometer scale with the same level of surety and control with which this can be done on the macroscopic scale. This article describes progress in using DNA as the medium for nanoconstruction.
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(1995)
Chem Intelligencer
, vol.1
, pp. 38-47
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-
Seeman, N.C.1
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4
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-
0020373595
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Nucleic acid junctions and lattices
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Seeman NC. Nucleic acid junctions and lattices. J Theor Biol. 99:1982;237-247.
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(1982)
J Theor Biol
, vol.99
, pp. 237-247
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-
Seeman, N.C.1
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6
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0028894215
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The topology of the kinetoplast DNA network
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of special interest. Kinetoplast DNA is a network containing several thousand minicircles that are topologically interlocked. The authors use a graph theoretical approach to provide precise models of possible network structures and their breakage patterns. By comparing these models with the results of cleavage analysis, the authors conclude that the structure is a honeycomb arrangement, with each minicircle positioned at the vertex of a hexagonal cell.
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of special interest Chen J, Rauch CA, White JH, Englund PT, Cozzarelli NR. The topology of the kinetoplast DNA network. Cell. 80:1995;61-69 Kinetoplast DNA is a network containing several thousand minicircles that are topologically interlocked. The authors use a graph theoretical approach to provide precise models of possible network structures and their breakage patterns. By comparing these models with the results of cleavage analysis, the authors conclude that the structure is a honeycomb arrangement, with each minicircle positioned at the vertex of a hexagonal cell.
-
(1995)
Cell
, vol.80
, pp. 61-69
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-
Chen, J.1
Rauch, C.A.2
White, J.H.3
Englund, P.T.4
Cozzarelli, N.R.5
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7
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0029562069
-
Changes in network topology during the replication of kinetoplast DNA
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of special interest. Kinetoplast DNA is a network containing ∼5000 minicircles that are topologically interlocked. The authors show that during replication, the minicircles are released from the interior of the network, nicked or gapped progeny minicircles are synthesized, and the progeny are attached to the periphery of the network, generating a Form II network of 10 000 nicked or gapped minicircles.
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of special interest Chen J, Englund PT, Cozzarelli NR. Changes in network topology during the replication of kinetoplast DNA. EMBO J. 14:1995;6339-6347 Kinetoplast DNA is a network containing ∼5000 minicircles that are topologically interlocked. The authors show that during replication, the minicircles are released from the interior of the network, nicked or gapped progeny minicircles are synthesized, and the progeny are attached to the periphery of the network, generating a Form II network of 10 000 nicked or gapped minicircles.
-
(1995)
EMBO J
, vol.14
, pp. 6339-6347
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Chen, J.1
Englund, P.T.2
Cozzarelli, N.R.3
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9
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0027976259
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DNA sequencing by hybridization
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of special interest. One of the interesting and unconventional suggestions for determining DNA sequences is to apply hybridization to an array of all possible oligonucleotides. The author assesses the feasibility of this approach in the light of experimental results.
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of special interest Mirzabekov AD. DNA sequencing by hybridization. Trends Biotechnol. 12:1995;27-32 One of the interesting and unconventional suggestions for determining DNA sequences is to apply hybridization to an array of all possible oligonucleotides. The author assesses the feasibility of this approach in the light of experimental results.
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(1995)
Trends Biotechnol
, vol.12
, pp. 27-32
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Mirzabekov, A.D.1
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11
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0028114541
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Molecular computation of solutions to combinatorial problems
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Adleman LM. Molecular computation of solutions to combinatorial problems. Science. 266:1994;1021-1024.
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(1994)
Science
, vol.266
, pp. 1021-1024
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Adleman, L.M.1
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12
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0029278612
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DNA solution of hard computational problems
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of special interest. of special interest. The author generalizes Adleman's result [11] and shows that DNA can be used to solve hard, NP-complete computational problems, such as the satisfaction of a group of logical statements. He demonstrates that, in principle, this can be achieved by a series of extraction and combination steps.
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of special interest Lipton RJ. DNA solution of hard computational problems. of special interest Science. 268:1995;542-545 The author generalizes Adleman's result [11] and shows that DNA can be used to solve hard, NP-complete computational problems, such as the satisfaction of a group of logical statements. He demonstrates that, in principle, this can be achieved by a series of extraction and combination steps.
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(1995)
Science
, vol.268
, pp. 542-545
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Lipton, R.J.1
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13
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0345200562
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R.J. Lipton, Baum E.B. American Mathematical Society. This book contains the proceedings of a meeting held in Princeton, New Jersey in April 1995. It summarizes virtually all of the work that had been done on DNA-based computing up to that time.
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Lipton RJ, Baum EB. DNA Based Computers Providence. 1996;American Mathematical Society, This book contains the proceedings of a meeting held in Princeton, New Jersey in April 1995. It summarizes virtually all of the work that had been done on DNA-based computing up to that time.
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(1996)
DNA Based Computers Providence
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14
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84959678845
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A mechanism for gene conversion in fungi
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Holliday R. A mechanism for gene conversion in fungi. Genet Res. 5:1964;282-304.
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(1964)
Genet Res
, vol.5
, pp. 282-304
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Holliday, R.1
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15
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0002012884
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DNA branch migration
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of special interest. Branch migration is an isomerization that can spontaneously relocate the site of the branch point in Holliday junctions. The authors describe the effects of solution conditions and heterology on the process and analyse mechanistic models that have been presented.
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of special interest Hsieh P, Panyutin IG. DNA branch migration. Nucleic Acids Mol Biol. 9:1995;42-65 Branch migration is an isomerization that can spontaneously relocate the site of the branch point in Holliday junctions. The authors describe the effects of solution conditions and heterology on the process and analyse mechanistic models that have been presented.
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(1995)
Nucleic Acids Mol Biol
, vol.9
, pp. 42-65
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Hsieh, P.1
Panyutin, I.G.2
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16
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0025635653
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De novo design of sequences for nucleic acid structure engineering
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Seeman NC. De novo design of sequences for nucleic acid structure engineering. J Biomol Struct Dyn. 8:1990;573-581.
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(1990)
J Biomol Struct Dyn
, vol.8
, pp. 573-581
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Seeman, N.C.1
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19
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0021995477
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Macromolecular design, nucleic acid junctions and crystal formation
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Seeman NC. Macromolecular design, nucleic acid junctions and crystal formation. J Biomol Struct Dyn. 3:1985;11-34.
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(1985)
J Biomol Struct Dyn
, vol.3
, pp. 11-34
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Seeman, N.C.1
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20
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0011840970
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The interactive manipulation and design of macromolecular architecture utilizing nucleic acid junctions
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Seeman NC. The interactive manipulation and design of macromolecular architecture utilizing nucleic acid junctions. J Mol Graph. 3:1985;34-39.
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(1985)
J Mol Graph
, vol.3
, pp. 34-39
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Seeman, N.C.1
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21
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0025804117
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The synthesis from DNA of a molecule with the connectivity of a cube
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Chen J, Seeman NC. The synthesis from DNA of a molecule with the connectivity of a cube. Nature. 350:1991;631-633.
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(1991)
Nature
, vol.350
, pp. 631-633
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Chen, J.1
Seeman, N.C.2
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22
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0000530422
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A solid-support methodology for the construction of geometrical objects from DNA
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Zhang Y, Seeman NC. A solid-support methodology for the construction of geometrical objects from DNA. J Am Chem Soc. 114:1992;2656-2663.
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(1992)
J Am Chem Soc
, vol.114
, pp. 2656-2663
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Zhang, Y.1
Seeman, N.C.2
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23
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0028003579
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The construction of a DNA truncated octahedron
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Zhang Y, Seeman NC. The construction of a DNA truncated octahedron. J Am Chem Soc. 116:1994;1661-1669.
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(1994)
J Am Chem Soc
, vol.116
, pp. 1661-1669
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Zhang, Y.1
Seeman, N.C.2
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24
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0001491398
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Bulged 3-arm DNA branched junctions as components for nanoconstruction
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Liu B, Leontis NB, Seeman NC. Bulged 3-arm DNA branched junctions as components for nanoconstruction. Nanobiol. 3:1994;177-188.
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(1994)
Nanobiol
, vol.3
, pp. 177-188
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Liu, B.1
Leontis, N.B.2
Seeman, N.C.3
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26
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0023055390
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Three arm nucleic acid junctions are flexible
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Ma R-I, Kallenbach NR, Sheardy RD, Petrillo ML, Seeman NC. Three arm nucleic acid junctions are flexible. Nucleic Acids Res. 14:1986;9745-9753.
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(1986)
Nucleic Acids Res
, vol.14
, pp. 9745-9753
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Ma R-I1
Kallenbach, N.R.2
Sheardy, R.D.3
Petrillo, M.L.4
Seeman, N.C.5
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27
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0024084223
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Ligation and flexibility of four-arm DNA junctions
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Petrillo ML, Newton CJ, Cunningham RP, Ma R-I, Kallenbach NR, Seeman NC. Ligation and flexibility of four-arm DNA junctions. Biopolymers. 27:1988;1337-1352.
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(1988)
Biopolymers
, vol.27
, pp. 1337-1352
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-
Petrillo, M.L.1
Newton, C.J.2
Cunningham, R.P.3
Ma R-I4
Kallenbach, N.R.5
Seeman, N.C.6
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28
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0026032501
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Stability and structure of three way DNA junctions containing unpaired nucleotides
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Leontis NB, Kwok W, Newman JS. Stability and structure of three way DNA junctions containing unpaired nucleotides. Nucleic Acids Res. 19:1991;759-766.
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(1991)
Nucleic Acids Res
, vol.19
, pp. 759-766
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Leontis, N.B.1
Kwok, W.2
Newman, J.S.3
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29
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0024262404
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DNA double-chain breaks in recombination of phage I and of yeast
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Thaler DS, Stahl FW. DNA double-chain breaks in recombination of phage I and of yeast. Annu Rev Genet. 22:1988;169-197.
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(1988)
Annu Rev Genet
, vol.22
, pp. 169-197
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Thaler, D.S.1
Stahl, F.W.2
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30
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0026019344
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Extensive 3′-overhanging single-stranded DNA associated with the meiosis-specific double-strand breaks
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Sun H, Treco D, Szostak JW. Extensive 3′-overhanging single-stranded DNA associated with the meiosis-specific double-strand breaks. Cell. 64:1991;1155-1161.
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(1991)
Cell
, vol.64
, pp. 1155-1161
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Sun, H.1
Treco, D.2
Szostak, J.W.3
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31
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0028972024
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Identification of double Holliday junctions as intermediates in meiotic recombination
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of outstanding interest. This is a key paper in the understanding of the structural chemistry of meiosis. The authors demonstrate that the branched-DNA molecules that arise as meiosis-specific double-stranded breaks are recombination intermediates which containing information from both parental chromosomes. These intermediates are resolved by Holliday into molecules containing both parental and recombinant duplexes.
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of outstanding interest Schwacha A, Kleckner N. Identification of double Holliday junctions as intermediates in meiotic recombination. Cell. 83:1995;783-791 This is a key paper in the understanding of the structural chemistry of meiosis. The authors demonstrate that the branched-DNA molecules that arise as meiosis-specific double-stranded breaks are recombination intermediates which containing information from both parental chromosomes. These intermediates are resolved by Holliday into molecules containing both parental and recombinant duplexes.
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(1995)
Cell
, vol.83
, pp. 783-791
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Schwacha, A.1
Kleckner, N.2
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32
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0027255843
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DNA double crossover structures
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Fu T-J, Seeman NC. DNA double crossover structures. Biochemistry. 32:1993;3211-3220.
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(1993)
Biochemistry
, vol.32
, pp. 3211-3220
-
-
Fu T-J1
Seeman, N.C.2
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33
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0028330515
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Holliday junction crossover topology
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Fu T-J, Tse-Dinh YC, Seeman NC. Holliday junction crossover topology. J Mol Biol. 236:1994;91-105.
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(1994)
J Mol Biol
, vol.236
, pp. 91-105
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-
Fu T-J1
Tse-Dinh, Y.C.2
Seeman, N.C.3
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34
-
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0028292141
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Symmetric Holliday junction crossover isomers
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Zhang S, Seeman NC. Symmetric Holliday junction crossover isomers. J Mol Biol. 238:1994;658-668.
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(1994)
J Mol Biol
, vol.238
, pp. 658-668
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-
Zhang, S.1
Seeman, N.C.2
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35
-
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0028330853
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Endonuclease VII cleavage of DNA double crossover molecules
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Fu T-J, Kemper B, Seeman NC. Endonuclease VII cleavage of DNA double crossover molecules. Biochemistry. 33:1994;3896-3905.
-
(1994)
Biochemistry
, vol.33
, pp. 3896-3905
-
-
Fu T-J1
Kemper, B.2
Seeman, N.C.3
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36
-
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0026443546
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DNA junctions, antijunctions and mesojunctions
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Du SM, Zhang S, Seeman NC. DNA junctions, antijunctions and mesojunctions. Biochemistry. 31:1992;10955-10963.
-
(1992)
Biochemistry
, vol.31
, pp. 10955-10963
-
-
Du, S.M.1
Zhang, S.2
Seeman, N.C.3
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37
-
-
0028934889
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Structural domains of DNA mesojunctions
-
of special interest. Junctions, mesojunctions and antijunctions are all unusual DNA topologies containing several connected double-helical domains that surround a unique point. The helix axes of junction domains are all radial (pointing at the point), and those of antijunction domains are all circumferential. Mesojunctions contain both radial and circumferential helical domains. The authors determine the structural features of mesojunctions containing even numbers of double-helical half-turns, and show their relationship to pseudoknots.
-
of special interest Wang H, Seeman NC. Structural domains of DNA mesojunctions. Biochemistry. 34:1995;920-929 Junctions, mesojunctions and antijunctions are all unusual DNA topologies containing several connected double-helical domains that surround a unique point. The helix axes of junction domains are all radial (pointing at the point), and those of antijunction domains are all circumferential. Mesojunctions contain both radial and circumferential helical domains. The authors determine the structural features of mesojunctions containing even numbers of double-helical half-turns, and show their relationship to pseudoknots.
-
(1995)
Biochemistry
, vol.34
, pp. 920-929
-
-
Wang, H.1
Seeman, N.C.2
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38
-
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0028232140
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DNA self-fitting: The double helix directs the geometry of its supramolecular assembly
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Timset Y, Moras D. DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. EMBO J. 13:1994;2737-2746.
-
(1994)
EMBO J
, vol.13
, pp. 2737-2746
-
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Timset, Y.1
Moras, D.2
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39
-
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0001690241
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Prediction of a crystallization pathway for Z-DNA hexanucleotides
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Ho PS, Kagawa TF, Tseng K, Schroth GP, Zhou G. Prediction of a crystallization pathway for Z-DNA hexanucleotides. Science. 254:1991;1003-1006.
-
(1991)
Science
, vol.254
, pp. 1003-1006
-
-
Ho, P.S.1
Kagawa, T.F.2
Tseng, K.3
Schroth, G.P.4
Zhou, G.5
-
40
-
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0029027735
-
An A-DNA triplet code: Thermodynamic rules for predicting A- and B-DNA
-
of special interest. The authors show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From the surface free energies estimated, they calculate a propensity for each DNA triplet to form A- or B-DNA. The agreement is particularly good in crystals.
-
of special interest Basham B, Ho PS. An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. Proc Natl Acad Sci USA. 92:1995;6464-6468 The authors show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From the surface free energies estimated, they calculate a propensity for each DNA triplet to form A- or B-DNA. The agreement is particularly good in crystals.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 6464-6468
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-
Basham, B.1
Ho, P.S.2
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42
-
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0025900334
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The construction of 3-D stick figures from branched DNA
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Seeman NC. The construction of 3-D stick figures from branched DNA. DNA Cell Biol. 10:1991;475-486.
-
(1991)
DNA Cell Biol
, vol.10
, pp. 475-486
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-
Seeman, N.C.1
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43
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0000588140
-
The design and synthesis of a knot from single-stranded DNA
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Mueller JE, Du SM, Seeman NC. The design and synthesis of a knot from single-stranded DNA. J Am Chem Soc. 113:1991;6306-6308.
-
(1991)
J Am Chem Soc
, vol.113
, pp. 6306-6308
-
-
Mueller, J.E.1
Du, S.M.2
Seeman, N.C.3
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45
-
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0001229034
-
Synthetic DNA knots and catenanes
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Seeman NC, Chen J, Du SM, Mueller JE, Zhang Y, Fu T-J, Wang H, Wang Y, S Zhang S. Synthetic DNA knots and catenanes. New J Chem. 17:1993;739-755.
-
(1993)
New J Chem
, vol.17
, pp. 739-755
-
-
Seeman, N.C.1
Chen, J.2
Du, S.M.3
Mueller, J.E.4
Zhang, Y.5
Fu T-J6
Wang, H.7
Wang, Y.8
S Zhang, S.9
-
46
-
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0028837712
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A synthetic DNA molecule in three knotted topologies
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of special interest. The authors demonstrate that a synthetic single strand of DNA can be cyclized to form a circle, a trefoil knot with negative nodes, a figure-of-eight knot (containing two negative and two positive nodes) and a trefoil knot with positive nodes. Each of the two helical domains in the molecule can assume the B-conformation (negative nodes) or the Z-conformation (positive nodes), depending on the solution conditions at the time of ligation.
-
of special interest Du SM, Stollar BD, Seeman NC. A synthetic DNA molecule in three knotted topologies. J Am Chem Soc. 117:1995;1194-1200 The authors demonstrate that a synthetic single strand of DNA can be cyclized to form a circle, a trefoil knot with negative nodes, a figure-of-eight knot (containing two negative and two positive nodes) and a trefoil knot with positive nodes. Each of the two helical domains in the molecule can assume the B-conformation (negative nodes) or the Z-conformation (positive nodes), depending on the solution conditions at the time of ligation.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 1194-1200
-
-
Du, S.M.1
Stollar, B.D.2
Seeman, N.C.3
-
47
-
-
37049081661
-
A topological rubber glove obtained from a synthetic single stranded DNA molecule
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of special interest. A topological rubber glove is any structure whose molecular graph can be deformed to its mirror image, but cannot be deformed to have a symmetry presentation. A figure-of-eight knot synthesized from DNA is shown to be the first molecule to have this property, by virtue of having different sequences in its two helical domains.
-
of special interest Flapan E, Seeman NC. A topological rubber glove obtained from a synthetic single stranded DNA molecule. J Chem Soc Chem Commun. 1995;2249-2250 A topological rubber glove is any structure whose molecular graph can be deformed to its mirror image, but cannot be deformed to have a symmetry presentation. A figure-of-eight knot synthesized from DNA is shown to be the first molecule to have this property, by virtue of having different sequences in its two helical domains.
-
(1995)
J Chem Soc Chem Commun
, pp. 2249-2250
-
-
Flapan, E.1
Seeman, N.C.2
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49
-
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0000421603
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The design of single-stranded nucleic acid knots
-
Seeman NC. The design of single-stranded nucleic acid knots. Mol Eng. 2:1992;297-307.
-
(1992)
Mol Eng
, vol.2
, pp. 297-307
-
-
Seeman, N.C.1
-
50
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0028320765
-
The construction of a trefoil knot from a DNA branched junction motif
-
Du SM, Seeman NC. The construction of a trefoil knot from a DNA branched junction motif. Biopolymers. 34:1994;31-37.
-
(1994)
Biopolymers
, vol.34
, pp. 31-37
-
-
Du, S.M.1
Seeman, N.C.2
-
51
-
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0030039749
-
The ligation of triangles built from bulged three-arm DNA branched junctions
-
Qi J, Li X, Yang XP, Seeman NC. The ligation of triangles built from bulged three-arm DNA branched junctions. J Am Chem Soc. 118:1996;6120-6130.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 6120-6130
-
-
Qi, J.1
Li, X.2
Yang, X.P.3
Seeman, N.C.4
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52
-
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0030061199
-
Antiparallel DNA double crossover molecules as components for nanoconstruction
-
Li XJ, Yang XP, Qi J, Seeman NC. Antiparallel DNA double crossover molecules as components for nanoconstruction. J Am Chem Soc. 118:1996;6131-6140.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 6131-6140
-
-
Li, X.J.1
Yang, X.P.2
Qi, J.3
Seeman, N.C.4
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