AC Gentechnologie Heidrun Karlic 1 und Clemens Heitzinger 2 , 3 1 - - PowerPoint PPT Presentation

▶

Jan 17, 2023 191 likes •360 views

AC Gentechnologie Heidrun Karlic 1 und Clemens Heitzinger 2 , 3 1 Ludwig Boltzmann Institute for Leukemia Research and Cluster Oncology, Hanusch-Krankenhaus 2 Fakultt fr Mathematik und Geoinformation, TU Wien 3 School of Mathematical and

SLIDE 1

AC Gentechnologie

Heidrun Karlic1 und Clemens Heitzinger2,3

1Ludwig Boltzmann Institute for Leukemia Research and Cluster Oncology, Hanusch-Krankenhaus 2Fakultät für Mathematik und Geoinformation, TU Wien 3School of Mathematical and Statistical Sciences, Arizona State University KAV Danubia, 24 Oct 2017

SLIDE 2

Nanopores as sensors

Nanopores can be used as molecular sensors using the principle of a Coulter counter. Applications include

◮ next-generation DNA sequencing

(Oxford Nanopore Technologies),

[Quick et al. Real-time, portable genome sequencing for Ebola surveillance. Nature, 530:228–232, 2016.]

◮ marker-free detection of single

molecules.

[Burns et al. A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. Nature Nanotechnology, 6:152–156, 2016.]

http: //www2.technologyreview.com/article/427677/ nanopore-sequencing/ 2 of 14

SLIDE 3

Movie: nanopore sequencing

Movie

3 of 14

SLIDE 4

Nanopore sensors

Applied potential Association/ dissociation Diffusion Outflow Receptor Reservoir Cargo molecule

4 of 14

SLIDE 5

The basic continuum model: the drift-diffusion-Stokes-Poisson system

Drift-diffusion equations for ionic transport, (Navier-)Stokes equations for water transport, Poisson equation for electrostatic interactions. −∇ · (A∇V ) = q(c+ − c− + c+

m − c− m ),

∇ · J− = 0, ∇ · J+ = 0, J− = q(D−∇c− − µ−c−∇V − c−v), J+ = q(−D+∇c+ − µ+c+∇V + c+v), ∇P = η∆v − q(c+

m + c+ − c− m − c−)∇V ,

∇ · v = 0. We use 2D and 3D FE calculations to solve this system.

5 of 14

SLIDE 6

The force on the target molecules

Force consists of electrostatic and drag contributions: F(x) = Fel(x) + Fdrag(x), Fel(x) =

Eρ, Fdrag(x) =

∂M

n ·

−η
∇u + ∇u⊤

+ pI

−4 −2 2 4 X coordinate [nm] −10 −8 −6 −4 −2 2 Z coordinate [nm]

Fel(x)

−14.0 −13.6 −13.2 −12.8 −12.4 −12.0 −11.6 −11.2 −10.8

6 of 14

SLIDE 7

The force on the target molecules

Force consists of electrostatic and drag contributions: F(x) = Fel(x) + Fdrag(x), Fel(x) =

Eρ, Fdrag(x) =

∂M

n ·

−η
∇u + ∇u⊤

+ pI

−4 −2 2 4 X coordinate [nm] −10 −8 −6 −4 −2 2 Z coordinate [nm]

Fdrag(x)

−16.0 −15.5 −15.0 −14.5 −14.0 −13.5 −13.0 −12.5 −12.0

6 of 14

SLIDE 8

DNA-origami nanopore: the force acting on the target molecules

Velocity of liquid Electrostatic and drag force

7 of 14

SLIDE 9

Validation by comparison with experimental data

−100 −50 50 100

Voltage Bias [mV]

−150 −100 −50 50 100 150

Current [pA]

PNPS 0.0 mC/m2 PNPS −40.0 mC/m2 PNPS −80.0 mC/m2 ref.

8 of 14

SLIDE 10

Movie: nanopore as single-molecule sensor

Movie

9 of 14

SLIDE 11

Continuum formulation of exit-time problem

From the Langevin equation dx dt = √ 2Dξt + D kT F(x), the backward Fokker-Planck equation ∂tp = ∇ · (D∇p) + D kT F · ∇p can be derived. Here p(x, t) is the probability that particle has exited.

10 of 14

SLIDE 12

Exit-time problem: continuum solution

Probability of successful exit: start point z nanometers above the pore and translocate pore within [0, t] without hitting boundary far away above pore.

50 100 150 z [nm] 0.0 0.2 0.4 0.6 0.8 1.0 p(x, t)

t = 0.00474890026424 [s]

Probability calculated here by solving the backward Fokker-Planck equation with Dirichlet boundary condition (1 means success, 0 means failure) and zero Neumann boundary conditions everywhere else.

11 of 14

SLIDE 13

Ausblick

Technologischer Fortschritt in der Gentechnologie betrifft mehrere Schritte:

◮ Lesen (d.h. Sequenzieren):

seit Jahrzehnten möglich, wird noch billiger werden

◮ Verstehen (Zusammenhang Genotyp-Phänotyp):

daran wird gearbeitet, z.B. im GTEx-Projekt (genotype-tissue expression)

◮ Editieren:

seit kurzem möglich, z.B. CRISPR

◮ Schreiben (d.h. Gensynthese):

das nächste Ziel

12 of 14

SLIDE 14

Ethische Fragen

◮ Für Fortschritte in der personalisierten Medizin ist es notwendig, große

(anonymisierte) Datenmenge (inkl. DNA-Sequenzen) zusammenzuführen und auszuwerten. Soll dafür die Zustimmung der Patienten notwendig sein? Wem gehören die Daten?

◮ Die Kosten mancher Therapien werden substantiell sein.

Wird man sich die Kosten leisten können? Wer wird bezahlen?

◮ Durch Schreiben synthetischer Gene wird man neue Organismen

erschaffen können. Soll das Editieren und Schreiben von Genen erlaubt sein? In welchen Fällen und für welche Organismen soll es erlaubt sein?

13 of 14

SLIDE 15

Danke für Eure Aufmerksamkeit! Fragen?

Clemens.Heitzinger@gmail.com http:/ /Clemens.Heitzinger.name/ HeidrunKarlic@gmail.com http:/ /drkarlic.com

14 of 14