H IGH -F IDELITY DNA H YBRIDIZATION USING P ROGRAMMABLE M OLECULAR DNA D EVICES Nikhil...
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Transcript of H IGH -F IDELITY DNA H YBRIDIZATION USING P ROGRAMMABLE M OLECULAR DNA D EVICES Nikhil...
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HIGH-FIDELITY DNA HYBRIDIZATION USING PROGRAMMABLE MOLECULAR DNA DEVICES
Nikhil Gopalkrishnan, Harish Chandran & John Reif
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FIDELITY OF HYBRIDIZATION
Perfect hybridization
Mismatched hybridization
Difference in energy between red strand hybridization and green strand hybridization is
small
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FIDELITY OF HYBRIDIZATION
Hybridization fidelity depends on length Errors in hybridization
Noise: Strands with sequence similar to the target
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DRAWBACKS OF LOW FIDELITY: SELF-ASSEMBLY
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DRAWBACKS OF LOW FIDELITY: SELF-ASSEMBLY
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DRAWBACKS OF LOW FIDELITY: DNA MICROARRAYS
From: http://en.wikipedia.org/wiki/File:NA_hybrid.svg
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EXACT HIGH-FIDELITY HYBRIDIZATION
Solution: ensemble of distinct sequences Target sequence s
Problem statement: Completely hybridize allcopies of s and don’t hybridize any other sequence
Multiple strands may bind to s and cooperatively hybridize it
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EXACT HIGH-FIDELITY HYBRIDIZATION
Solution: ensemble of distinct sequences Target sequence s
Problem statement: Completely hybridize all copies of s and don’t hybridize any other
sequence Multiple strands may bind to s and
cooperatively hybridize it Completion of hybridization should be
detectable Example: by fluoroscence
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APPROXIMATE HIGH-FIDELITY HYBRIDIZATION
Hybridization Error At most b bases may mismatch: b-hybridized
Success probability probability of b-hybridization at least p
Problem statement: b-hybridize each copy of s with probability at least p and no other sequence is b-hybridized with probability greater than 1-p
p ≈ 95% and b ≈ 1/10th of length of s
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ASSUMPTIONS
Short sequences have high fidelity of hybridization
Subsequences sequestered in short hairpins are unreactive
Strand displacement occurs whenever possible and proceeds to completion
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APPROXIMATE HIGH-FIDELITY HYBRIDIZATION
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NOTATION
Letters represent sequences Example: ci
Sequences concatenate ci = ai bi
Written from 5’ to 3’ Sequences differing only in the subscript are
concatenations of subsequences differing only in the subscript ci = ai+1 bi implies ci+1 = ai+2 bi+1
Bar indicates reverse complement ci = bi ai is the reverse complement of ci = ai bi
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 1ST PROTOCOL
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1ST PROTOCOL: POTENTIAL SOURCE OF ERROR
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1ST PROTOCOL: POTENTIAL SOURCE OF ERROR
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1ST PROTOCOL: POTENTIAL SOURCE OF ERROR
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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HIGH-FIDELITY HYBRIDIZATION: 2ND PROTOCOL
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FAVORABLE PROPERTIES OF THE PROTOCOLS
Autonomous Fluorophore based detection
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SIMULATION OF FINITE AUTOMATA
Finite automata: Mathematical constructs that define languages
Limited computational power Memoryless
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SIMULATION OF FINITE AUTOMATA
Target strand encodes input to automata Checker sequences perform state transitions
Green sequence performs δ(y,0) = z
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SIMULATION OF FINITE AUTOMATA
Incorrect checker sequence may attach Further attachment is blocked as second hairpin
doesn’t open At each step, probability of correct
attachment ≥ 0.5 Probability of successful completion ≥ 1/2 n
where n=size of i/p Can process multiple inputs in parallel Number of checker sequences ≤ Twice
number of edges in the transition diagram of the automata
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PROTOCOL KINETICS
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FUTURE WORK
Experimental verification for a simple case with just two checker sequences
Computer simulation to predict reaction kinetics