馬 渕研 究 室
Biomolecular Flow Systems Laboratory

生体分子流動システム研究分野

Visualizing the Molecular World
When small molecules, particularly ions, transport through complexly intertwined structures, what paths do they takeand how fast can they move (conduct or diffuse)? Ion transport phenomena occurring in the nanoscale world play a
crucial role in a wide range of fields, from biomolecules in life sciences to polymer materials in materials science.
We use theoretical approaches (e.g., molecular simulations) to elucidate these phenomena, which are difficult toobserve in experiments, on challenging spatiotemporal scales. Our goal is to perform theoretical high-efficiency andhigh-functionality molecular design, and, in collaboration with experimental groups, we aim for broad applications
ranging from engineering applications, such as constructing artificial cells and molecular systems, to medicalapplications, including drug discovery.

K+ selective transport by artificial DNA channel
Ion channels exist in the cell membrane and have the function of regulating ion transport. Artificial ion channels thatmimic the function of ion channels and have applications in medicine and engineering are attracting attention.
Therefore, we aim to design a mechanism to control ion transport by artificial DNA channels by modifying functionalgroups inside the artificial DNA channels and elucidating the transport mechanism.
Ion channels

Ion channel

Ion Transport Control by Artificial DNA Channel

Mimics the transport
function of ion channels

Cellmembrane

Using artificial DNA channel, the effects of functional groups inside the channel
on ion transport were investigated for the development of K+ sensors.

Pass

Block

Water＋KCl

Design of Artificial Ion Channels

Block

Medical ScienceCell

Drug Delivery

Cl－Engineering

Lipids90°

Biosensor
Water FiltrationDNALipids
channelWater＋KClK＋

DNA nanotechnology
Innovative molecular technology that uses sequence-specific molecular assemblyand periodic structure of DNA to design and create nanoscale structures.
Basic Structure

PO4－Advantages

DesignCreate
Nature 2006, 440, 297–302

K＋：Functional group modifications

Single nucleotide design
Modifications of other molecules

PO4－Hexyl groupEthyl groupEthyl group

Hexyl group

Results
Functional groups reduce transport
Enables selective transport to K+

Molecular uptake by liquid-liquid phase separation (LLPS)
Liquid-liquid phase separation (LLPS) is a phenomenon wherein biomolecules self-assemble under specificcondition to form droplets, which holds potential applications in drug delivery. We aim to theoretically design
artificial peptide molecules that can selectively uptake target molecules, using elastin-like polypeptides (ELP) as abase material to evaluate the uptake of small molecules into droplets.
Biomolecular uptake by VPGVG coacervate
Liquid‒liquid phase separation (LLPS)
Condition: Temperature, pH, Molecular Concentration etc.
Role of LLPS
LLPS
Signal transduction at the cell

Evaluation of VPGVG coacervation(2.1kDa at 5wt%)(8.6kDa at 5wt%)

Coacervation×

Coacervation〇Effect of Molecular Weight/Polymer
Chain on VPGVG Coacervation

membraneAggregated protein formation
Storing DNAReversiblereaction

Molecule B

Fluid in droplet→ Mass transfer insideand out of droplets

CellO

NHNN
H

H
N

ssRNA

ssRNAETLLPS induced bytemperature risen(VPGVG)n

LLPS

ELP’s property

OOHNODNARNA uptake energy of VPGVG

Molecule A

Elastin-like polypeptides(ELPs)
OHydrophobic/hydrophilic RNA uptake

TemperatureriseBiocompatibility
Dehydration

Relatively easy toprepare
50 µm

V: Valine, P: Proline, G: Glycine, n: peptides length

50 µmResults
The coacervation of VPGVG depends on molecular weight andpolymer chain length.
Hydrophobic ssRNAET is more easily incorporated.

EventsExchange meeting withcollaborators

Associate Professor
Takuya MABUCHI

Cherry-blossom viewing
Internship
Recognition event

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