Introduction to Biocomputing: DNA
Computing I
Image Courtesy of Liang Zong and Yan Liang
Alfonso Rodríguez-Patón
Universidad Politécnica de Madrid
Laboratorio de Inteligencia Artificial (LIA)
arpaton@fi.upm.es
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Syllabus
• 1. DNA Computing
– 1.1. DNA structure and DNA operations
– 1.2. DNA Strand displacement-based biocircuits
– 1.3. Molecular automata
– 1.4. Adleman experiment
• 2. Synthetic Biology: genetic circuits
– 2.1. Gene expression and regulation
– 2.2. Genetic Boolean logic gates
– 2.3. Basic genetic circuits: A toggle switch and an oscillator
(repressilator).
– 2.4. CRISPR-based devices and gene drives
• 3. Programmable Biology
– 4.1. Automation in Biology
– 4.2. Simulating bacterial colonies with IBM: Gro simulator
– 4.3. Engineering portable biolabs with Arduino cards and software
blocks.
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Assesment activities
• Exam (written; basic concepts; pass or fail).
• Oral presentation (10 minutes; by pairs or
trios). 20% of the final evaluation
• Final work: essay or cellular simulation (with
gro, Matlab, etc.). (individual work). 80%
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• Professors:
– Alfonso Rodríguez-Patón
– Daniel Manrique
• PostDocs:
– Tao Song
• PhD students:
– Elena Núñez
– Marcos Rodríguez
– Tongmao Ma
– Lucía León
– David Méndez
arpaton@fi.upm.es
• Master students, practicum
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Outline of the class
DNA Computing:
DNA: structure and operations
Basic DNA circuits
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DNA Computing (Biomolecular Computing)
q DNA Computing (Biomolecular Computing): Design and
engineering of programmable biomolecular devices with new
abilities to process biomolecular information. Using biomolecules to
process information encoded in biomolecules ADN, ARN y proteinas
q Why compute with DNA? To program/control biomolecular
devices
q Why might be more useful a biomolecular computer than
electronics? For biomolecular information processing in vitro or in
vivo. To operate within a cell or a living organism. computador biomolecular ->
procesar info biomolecular
(naturales o codificada)
En esa epoca se podia secuenciar la cadena de adn -> se dieron cuenta de q se podía escribir (caro)
Operaciones -> cortar, dividr segun subcadenas...
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What is DNA?
• Deoxyribonucleic acid (DNA): a molecule
inside living cells that encode all the
information that allow that cell to live and
reproduce. DNA is the molecule used to write
the operating system of a cell: the genome.
• DNA is written using an alphabet of 4 letters
called bases or nucleotides: A, C, G, T
doble helice
• (RNA is similar: U instead of T)
1 tira
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Bioinformatics schematic of a cell
Macromolecule Monomer
(Polymer)
DNA Deoxyribonucleotides
(dNTP)
RNA Ribonucleotides (NTP)
Protein or Polypeptide Amino Acid
Watson and Crick
Nucleic acids (DNA and RNA)
• Form the genetic material of all living
organisms.
• Found mainly in the nucleus of a cell (hence
“nucleic”)
• Contain phosphoric acid as a component
(hence “acid”)
• They are made up of nucleotides.
Nucleotides
• A nucleotide has 3 components
– Sugar (ribose in RNA, deoxyribose in DNA)
– Phosphoric acid
– Nitrogen base
• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Thymine (T) or Uracil (U)
Monomers of DNA
• A deoxyribonucleotide has 3 components
– Sugar - Deoxyribose
– Phosphoric acid
– Nitrogen base
• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Thymine (T)
Monomers of RNA
• A ribonucleotide has 3 components
– Sugar - Ribose
– Phosphoric acid
– Nitrogen base
• Adenine (A) A-U
G -C
• Guanine (G)
• Cytosine (C)
• Uracil (U)
Nucleotides
Phosphate Nitrogenous
Base
Group
Sugar
Phosphate Nitrogenous
Base
Group
Sugar
DNA RNA
A T A
A=T
G C G=C G
C G C
G C G
A T A
C G T®U C
T A U
G C G
DNA structure
Watson-Crick
complementarity
A–T
C–G
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Hybridization by Watson-Crick base
complementarity
A T C G C T
T A G C G A
al ser complementarias, si stan separadas y se juntan -> se hibridan por ser complementarias
Se pueden separar aplicando calor para romper los enlaces de H, si se enfria y se encuentran se hibridan
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Operations with DNA
• Synthesize (write DNA), sequence (read DNA).
• Hybridization of complementary bases. Se enfria se hibridan
• Denaturation. Aplicar calor para separarlos
• Cut. enzimas de restricción -> proteinas q detectan secuencia de adn -> se junta y cortan el adn
• DNA separation by length. Gel electrophoresis.
• Extraction.
• Polymerization with DNA Polymerase. encima capaz de copiar el adn
tambn arn polimerasa (virus)
Transcriptasas inversa -> de
• PCR amplification (DNA Photocopy). ADN a ARN
PCR -> copiar cadena de adn de forma exponencial con ciclos de calor enfriado para q se separen las hebras, se unen
las adn polimerasas, hacen la copia y se unen los cebadores q le indica por donde empezar a copiar -> 2^n en
segundos
se pueden reensamblar distintos fragmentos del adn con enzimas de restriccin especificos q generan extremos23
coesivos
Hybridization and renaturation
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Hybridization and renaturation
A T C G C
T A G C G
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Separation, detection, extraction
• Hybridization probes: “search method” or detection
of specific DNA sequences.
Probe: Small single-stranded strand complementary of the
searched strand.
1. Denaturation of the target strands .
2. Add a `labeled’ tube and allow hybridization.
3. Examine whether the hybridization has occured and the
extraction of the pair probe.
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Copying a DNA sequence: DNA Polymerase
ALTA FIABILIDAD
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Polymerase chain reaction (PCR)
ADN Polimerasa
ADN objetivo
3' 5'
5' 3' Cebadores
3' 5' 5' 3'
Desnaturalizar
el ADN
Primer ciclo
Hibridación de
los cebadores
5' 3'
Extensión de las 5' 5'
nuevas hebras 3' 5'
2 copias en el
primer ciclo
Desnaturalizar
el ADN
Hibridación
de los cebadores
Segundo ciclo
Extensión de las
nuevas hebras
4 copias en el
segundo ciclo
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Gel Electrophoresis
Separation of DNA strands by length
Se añade colorante y el ADN se tiñe -> se aplica campo electrico -> ADN migra al positivo
Electrode Samples
Slower
Gel
Buffer
Electrode
Faster
Los geles stan calibrados de tal forma q se sepa cuanto va a tardar el adn en migrar en funcion del tamaño
Por eso se separan el ADN por longitud y se puede extraer el ADN por longitud al saber donde sta 29
Outline of the talk
1. DNA Computing:
1. DNA: structure and operations
2. Basic DNA circuits
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DNA sensing based on strand displacement
Sensing the presence of a DNA/RNA strand A
B
DNA strand A
Input A’
Strand Competitive
displacement hybridization
B
A
Output
A’
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Logic DNA sensor/actuator
Patente del grupo LIA
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DNA Computing: biomolecular automaton
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