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Protein-DNA Computation by Stochastic Assembly Cascade

Protein-DNA Computation by Stochastic Assembly Cascade. Roy Bar-Ziv, Tsvi Tlusty, and Albert Libchaber PNAS Sep.3, 2002 Presented by Je-Gun Joung. Overview. The assembly of RecA on single-stranded DAN is measured and interpreted as a stochastic finite-state machine

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Protein-DNA Computation by Stochastic Assembly Cascade

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  1. Protein-DNA Computation by Stochastic Assembly Cascade Roy Bar-Ziv, Tsvi Tlusty, and Albert Libchaber PNAS Sep.3, 2002 Presented by Je-Gun Joung

  2. Overview • The assembly of RecA on single-stranded DAN is measured and interpreted as a stochastic finite-state machine • This machine is able to discriminatefine differencesbetween sequences • In vivo stochastic biomolecular computation based on low-specificity protein-DNA binding

  3. Molecular Machine by Stochastic Assembly Cascade • Hardware • A test tube filled with a solution of single-stranded DNA molecule, RecA protein, and ATP molecules • Output device (molecular machine reporters): a change in the rotational motion of the DNA molecule • Software • Two basic operation: nucleation and disassembly • Chang the machine’s internal state (the current length of RecA)

  4. Q0 Q1 Q2 …… QN QN-1 Molecular Machine by Stochastic Assembly Cascade RecA ATP ssDNA Output device (fluorescence anisotropy) Two basic operation (nucleation and disassembly) Hardware Software

  5. RecA • The protein responsible for recombination in bacteria RecA RecA coats ssDNA Alignment with homologous DNA sequence 5’ 3’ ssDNA 3’ Formation of joint chromosomal DNA 5’ 5’ 3’

  6. RecA RecA Monomer RecA/Rad51 DNA Filaments

  7. Biochemistry of RecA Assembly • Nucleation (assembly): extend the filament by long chunks 5’ 3’ TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC • Disassembly: removes monomers one by one 3’ 5’ TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC

  8. Q0 Q1 Q2 …… QN QN-1 Simulation of a 26-state Stochastic Assembly Cascade

  9. ……… QN QN-1 Q2 Q1 Q0 A Deterministic Reading Head Changes its Internal State dn : disassembly from state Qn en : nucleation to state Qn x: noting happens Reading Head Q6 ……… x e8 x d8 d7 x x d6 d5 x e9 d9 x Tape

  10. A Simple Set of Rules Suppose that the machine is at state Qn • If it read dn, it moves to state Qn+1 • If it read em and m < n the machine moves to state Qm • In all other cased, if it read x and dm with m n, or em with m n, then it stays at stateoves to state Qn

  11. “Sequence-detector” Machine • Assembly cascades on single-stranded DNAs on 39 or 78 bases long (13- and 26-stage machines) • Infer its internal dynamics from observable output • A sufficient set of observations to overcome the noisiness of the output •  105-106 fluctuating DNA-RacA complexes • A very smooth ensemble-average signal

  12. An Exponential Sensitivity of the Assembly Cascade • Both curves decay exponentially close to saturation with a higher slope for the longer sequence that has more cascade stages • A: fluorescence anisotryopy • S: the normalized anisotropy • Open circles: (TAC)13 • Triangles: (TAC)26

  13. Sequence-Discrimination Capability Localized differences in nonuniform sequences Very similar triplet repeats DA: the difference between the fluorescence anisotropy signal

  14. Discussion • By choice of other types of sequence base vectors, the stochastic cascade machinery can encode and decode mixtures in terms of other transforms • Additional operations to manipulate sequences such as recombination • The question of whether RecA assembly is used for natural computation requires in vivo testing.

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