Simulation and Analysis of in vitro DNA Evolution

Physical Review Letters

Volumn 92, Issue 3, 2004, Pages 381011-381014

  Kloster, Morten ^a,b   Tang, Chao ^b,c  

^a PRINCETON UNIVERSITY   (United States)

^b NEC LABORATORIES AMERICA   (United States)

^c PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOTECHNOLOGY; COMPUTER SIMULATION; ERROR ANALYSIS; ITERATIVE METHODS; MOLECULAR BIOLOGY; MUTAGENESIS; PARAMETER ESTIMATION; PROBABILITY; PROTEINS; RANDOM PROCESSES; SET THEORY;

DNA TRANSCRIPTION FACTOR; MEAN FIELD (MF) BEHAVIOR; POLYMERASE CHAIN REACTION (PCR);

DNA SEQUENCES;

DNA; NUCLEAR PROTEIN; PROTEIN BINDING;

BIOLOGICAL MODEL; GENETICS; KINETICS; METABOLISM; MOLECULAR EVOLUTION; MUTATION; SUPPRESSOR GENE;

DNA; EVOLUTION, MOLECULAR; GENES, SUPPRESSOR; KINETICS; MODELS, GENETIC; MUTATION; NUCLEAR PROTEINS; PROTEIN BINDING;

EID: 1442355620     PISSN: 00319007     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (17)

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2. L. F. Landweber, Trends Ecol. Evol. 14, 353 (1999).
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6. Enrichment (i.e., sequences very close to WT [7] in the initial pool being amplified exponentially) was crucial for the observed evolution dynamics in [5], as the authors started from a mix of random DNA sequences.
7. We let WT denote the highest affinity sequence, although this is not the actual wild type [5,8].
8. D. S. Fields, Y. He, A. Al-Uzri, and G. D. Stormo, J. Mol. Biol. 271, 178 (1997).
9. G. D. Stormo and D. S. Fields, Trends Biochem. Sci. 23, 109 (1998).
10. T.-K. Man and G. D. Stormo, Nucleic Acids Res. 29, 2471 (2001).
11. NSB. This binding dominates for DNA sequences very far from WT, but is negligible for the case studied in this Letter [12](we include it in simulations).
12. M. Kloster and C. Tang, cond-mat/0301372.
13. For molecules simultaneously mutated at multiple positions, we randomly assign an order to the mutations.
14. D. A. Kessler, H. Levine, D. Ridgway, and L. Tsimring, J. Stat. Phys. 87, 519 (1997).
15. For large N, almost all the WT comes from minimum paths (Fig. 1). To be safe, we allow one erroneous mutation and verify that this is a minor correction.
16. M. Kloster (unpublished).
17. D. Ridgway, H. Levine, and D. A. Kessler, J. Stat. Phys. 90, 191 (1998).