Hybrid Biomolecular Electronic Devices Dr Steve Johnson � Department of Electronics University of York �
What is Biomolecular Electronics Hybrid technology focused on the integration, detection and manipulation of biological molecules, such as DNA, proteins and peptides with electronic devices
Biological molecules primer Single stranded DNA Double stranded DNA Sugar deoxyribose one of the four possible DNA bases (ACTG) Phosphate group 1.2nm DNA bases acid part of DNA guanine cytosine O H 2 N N HN N NH 2.2nm NH N O NH 2 NH 2 O N NH HN N HN N O adenine thymine 1nm
Biological molecules primer Amino acid Carboxylic Primary structure acid Amine Tertiary structure Side chain variable Polypeptide Peptide Secondary bond structure Quaternary structure
Biomolecules: beyond biology Molecular recognition: spontaneous assembly of molecules driven by interactions between complementary biomolecules e.g. proteins & peptides e.g. DNA DNA tiles: Nadrian Seeman (1982) Video removed: See https://www.youtube.com/watch? v=X-8MP7g8XOE A. J. Olson: Scripps Research Institute DNA origami: Paul Rothemund 2006
Biomolecules for computation Molecular recognition between complementary biomolecules to store and process information encoded by the polymer sequence Why: Parallel processing ( 10 base DNA = 1 × 10 6 distinct sequences; 10 residue peptide = 1 × 10 13 ) High selectivity and low error rates - failure to function = death! Cost (synthetic DNA: £1 per base, synthetic peptide: £5 per reside) Integration with biological systems (e.g. smart drugs) DNA-based computing machines Toe-hold strand displacement Direct hybridisation Erik Wilkman J. Am. Chem. Soc. 131, 17303 (2009) Adleman Science, 266, 1021 (1994) 3 toe-hold 2* 2 1 2* 1* 2* Input 3 2* 1* 2 1 path (i-k) path (j-i) 2* 1* 2* 3 Output node (i) 2 1
Biomolecules for computation Strand displacement DNA logic Frezza JACS, 129, 14875 (2007)
Biomolecules for computation Molecular machines based on DNA hairpins Christina Santini et al. Chem. Comms. 49, 237 (2013) input + clock transition fuel/ clock
Biomolecules for computation Protein and peptide-based computing machines Computational machines theorised exploiting antibody-antigen interactions not yet realised due to lack of appropriate antibodies - synthetic antibody mimetics Peptide networks Enzymatic logic JACS, 126, 11140 (2004) J. Phys. Chem. A. 110, 8548 (2006) input 1 input 2 glucose H 2 O 2 NAD + GDH HRP glucose Horseradish output dehydrogenase peroxidase NADH input 1 input 2 output 0 0 0 0 1 1 1 0 1 input1: E 3 +N 0 XOR logic input2: E 4 +N 1 1 OR logic
Biomolecules for computation: Challenges Designing (programming) the machine: Particularly challenging for protein/ peptide based devices Reading the output: PCR, gel electrophoresis, fluorescence, mass spectrometry Integrating biological circuits: Incompatibility between input (DNA, peptide, protein, chemical) and output signals (biomolecular, chemical, fluorescent) Hybrid biomolecular electronics: � Direct (label-free) read-out � Integration via underlying electronics
Biomolecular electronics: Immobilisation I Immobilising DNA onto inorganic surfaces Stable, covalent surface attachment via thiol chemistry Thiolated short chain alkanes to present DNA and block exposed Au DNA − SH + Au → DNA − S − Au + H SH SH S S S S S S S S Au Au Au Regulating surface density of DNA Minimise steric hindrance - DNA hairpins clock clock S S S S S S
Biomolecular electronics: Immobilisation II Immobilising peptides/ proteins onto inorganic surfaces Pre-assembly of chemoselective, biocompatible monolayer J. Mat. Chem. B. submitted (2014) Images removed NH 2 PEG SH S S S S S S S S S S S S S S Au Au Au
Biomolecular electronics: Immobilisation II Protein orientation Anal. Chem. 80, 978 (2008) binding region Images removed S S S S S S S S S S S S S S S Au Au 0.3 (a) (b) 0.6 Mass (ng/mm2) 0.2 0.4 ligand 0.1 0.2 binding site 0.0 0.0 0 500 1000 1500 0 500 1000 1500 Time (s) Time (s)
Biomolecular electronics: Immobilisation III Immobilising biomolecules with high spatial resolution DNA: sub-50nm resolution Langmuir, 19, 981 (2003) Peptides: sub-100 nm resolution Nanotechnology, 23, 495304 (2012) 1 µ m
Biomolecular electronics: Detection I Electrochemical impedance spectroscopy (EIS) 0 –20 R s ϕ (z) (deg) –40 –60 R C mol mol –80 10 –1 10 0 10 1 10 2 10 3 10 4 Frequency (Hz) 0 –70 –20 R s ϕ (z) (deg) –40 –80 –60 R 10 –1 10 1 C mol mol –80 10 –1 10 0 10 1 10 2 10 3 10 4 Frequency (Hz)
Biomolecular electronics: Detection I Electrochemical impedance spectroscopy (EIS) Cell lysate: i.e. select specific protein out of cocktail of circ. 1M other proteins, DNA, RNA, fats, lipids, salts ... � Detection limit 50pM
Biomolecular electronics: Detection II Cyclic voltammetry: Redox DNA hairpins 2 e - 2 H + d Clock d S S Images removed
Biomolecular electronics: Regulation I Redox active systems E ox 6 = E red ? Langmuir , 28, 6632 (2012) Cu 2+ 1.5nm Cu 0.6 0.4 Au Au Cu 2+ Cu 2+ 0.2 I ( A) O O O O Cu 1+ 1.9nm OH OH OH OH Cu 0.0 C C C C e –0.2 Vpk –0.4 0.0 0.4 0.8 1.2 Ewe (V) 3 S S S S Au Au Au Au Thickness (nm) 2 1 0 Cu 1+ Cu 2+ Cu 1+ Cu 2+ Cu 1+ Cu 2+ Cu 1+
Biomolecular electronics: Regulation II Protein charge sensitive to local solution conditions e.g pH, ionic strength � e.g. pH sensitivity of HA protein of flu virus _ H + Low pH (High H + ) Mid-range pH High pH (Low H + ) Images removed
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