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АКТУАЛЬНЫЕ НАПРАВЛЕНИЯ СОВРЕМЕННОЙ НАУКИ : УГЛЕРОДНЫЕ НАНОТРУБКИ КАК ОСНОВА ДЛЯ СОЗДАНИЯ БИОСЕНСОРОВ. wrapped-DNA SWNT. Д.ф.-м.н. Виктор Алексеевич Карачевцев. ОТДЕЛ МОЛЕКУЛЯРНОЙ БИОФИЗИКИ Физико-технический институт низких температур НАН Украины им. Б. И. Веркина , Харьков.

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slide1

АКТУАЛЬНЫЕ НАПРАВЛЕНИЯ СОВРЕМЕННОЙ НАУКИ:

УГЛЕРОДНЫЕ НАНОТРУБКИ КАК ОСНОВА ДЛЯ СОЗДАНИЯ БИОСЕНСОРОВ

wrapped-DNA SWNT

Д.ф.-м.н. Виктор Алексеевич Карачевцев

ОТДЕЛ МОЛЕКУЛЯРНОЙ БИОФИЗИКИ

Физико-технический институт низких

температур НАН Украины

им. Б. И. Веркина, Харьков

karachevtsev@ilt.kharkov.ua

.

slide2

СОДЕРЖАНИЕВведение: углеродные нанотрубки – материал 21 векаЭлектронная структура углеродных одностенных нанотрубок (УОНТ).Спектроскопия ОУНТ: Рамановская спектроскопия, спектроскопия поглощения, люминесценция.Экспериментальное определение хиральности нанотрубок. Достоинства УОНТ при создании биосенсоров. Нековалентная фунционализация ОУНТ с помощью органических молекулИндивидуальные нанотрубки в водной суспензии – способ их приготовления: а) за счет образования мицеллб) благодаря воднорастворимым полимерам.Биосовместимость УОНТ посредством ДНК (однонитевой и двунитевой полимер).Наногибрид УОНТ:ДНК:фермент в качестве элемента люминесцентного сенсора для определения уровня глюкозыВыводы

carbon single walled nanotube
Carbon single-walled nanotube

Schematic representation of a 2D graphite layer with the lattice vectors a1 and a2 and the roll-up vector Ch_na1_ma2 . Achiral tubesexhibit roll-up vectors derived from (n,0) (zigzag) or (n,n) (armchair). Thetranslation vector T is parallel to the tube axis and defines the 1D unit cell.The rectangle represents an unrolled unit cell, defined by T and Ch. In thisexample, (n,m) =(4,2)

Chiral vector: Ch=na1+ma2=(n,m)

Nanotube diameters: d=31/2ac-c(m2+mn+n2)1/2/π

Chiral angle: θ=tan-131/2m(m+2n)

metallic conduction in (n,m) carbon nanotube is achieved when

2n+m = 3q

where q is an integer. 1/3 of the nanotubes are metallic and 2/3 are semiconducting

uv visable nir light absorption of swnts
UV-visable-NIR light absorption of SWNTs

metallic

E11

semiconducting

E22

E11

Light absorption of SWNT in NIR region is caused by electronic transitions between pairs of van Hove singularities. So, light absorption in the region 1800-1000 nm is assigned to electronic transitions E11S in the semiconducting nanotube (band gap transition), absorption at the energy 900-500 nm results from the E22S transitions of these types of SWNTs and absorption at 500-300 nm is assigned to the E11m transition in the metallic SWNTs.

slide7

Достоинства углеродных нанотрубок при построении сенсоров:а) химическая стойкость к воздействию различных агрессивных сред, а также в слабом влиянии на среду, в которой происходит диагностика, что особенно важно для биологических систем;б) термическая стойкость нанотрубок, которая может быть использована при регенерации сенсора;с) металлическая или полупроводниковая проводимость нанотрубок, которая значительно облегчает сам процесс создания сенсора на основе нанотрубок, поскольку она сама уже может являться элементом электронного устройства; д) размеры сенсора: одностенная нанотрубка имеет диаметр 0,5-2 нм и длину до нескольких мкм; е) разветленная поверхность (высокий показатель площади поверхности на единицу веса) - одностенная нанотрубка представляет собой углеродный монослой завернутый в цилиндр; ж) сверхпрочность.

network field effect transistors
Network Field-Effect Transistors

Schematic illustration of layouts for bottom-gate (a) and top-gate (b) SWNT TFT devices

dna decorated carbon nanotubes for chemical sensing
DNA-decorated carbon nanotubes for chemical sensing

A. T. C Johnson et al, phys. stat. sol. (b) 243, No. 13, 3252–3256 (2006)

We demonstrate a versatile class of nanoscale chemical sensors based on single-stranded DNA (ssDNA)for chemical recognition and single-walled carbon nanotube field effect transistors (SWNT FETs) forelectronic read-out. SWNT FETs with a nanoscale coating of ssDNA respond to vapors that cause no detectableconductivity change in bare devices. Sensor responses differ in sign and magnitude for differentgases and can be tuned by choice of the ssDNA base sequence. Sensors respond and recover rapidly (seconds),and the sensor surface is self-regenerating. Preliminary results of all-atom molecular dynamicssimulations agree with experiment.

slide11

Enzyme-Coated Carbon Nanotubes as Single-Molecule BiosensorsK.Besteman, J-O Lee, F.G. M. Wiertz, H.A. Heering, and C. DekkerNano Lett.,, 2003

color detection using chromophore nanotube hybrid devices
Color Detection Using Chromophore-Nanotube Hybrid Devices

A nanoscale color detector based on a single-walled carbon nanotube functionalized with azobenzene chromophores, where the chromophores serve as photoabsorbers and the nanotube as the electronic read-out. By synthesizing chromophores with specific absorption windows in the visible spectrum and anchoring them to the nanotube surface, it was demonstrated the controlled detection of visible light of low intensity in narrow ranges of wavelengths. These measurements are suggested that upon photoabsorption, the chromophores isomerize from the ground state trans configuration to the excited state cis configuration, accompanied by a large change in dipole moment, changing the electrostatic environment of the nanotube.

X.Zhou et al. Nano Lett., 2009, 9 (3), pp 1028–1033

Sandia National Laboratories, Livermore,

dependence of energy separation between van hoff singularities from swnts diameters
Dependence of energy separation (between van Hoff singularities) from SWNTs diameters.

For the each laser excitation energy the two lowest energy transitions are correspond to semiconducting nanotubes, the next higher energy transition is for metallic NT and so on. So, in Raman measurements the resonance condition will be occurred for nanotubes certain diameters.

slide14
Спектры комбинационного рассеяния одностенных углеродных нанотрубок.

A1g

E1g

A1g

He-Ne лазер з λexc=632.8 нм (1,96 еВ)

swnts aggregate in bundles as a result of substantial van der waals attractions between tubes
SWNTs aggregate in bundles as a result of substantial van der Waals attractions between tubes

bar 10nm

bar 500nm

R Smalley et al, J. Phys. Chem. 2001

Unfortunately, nanotubes are poorly soluble in the most of organic solvents and are insoluble in water. This is because NTs aggregate in bundles as a result of substantial van der Waals attractions between tubes. Solution nanotubes in water is realized if a surfactant or polymer is added into aqueous solution. Sonication of an aqueous SWNT solution containing a polymer can lead to debundled isolated SWNTs. Polymer wrapped around tubes can preclude its aggregation in bundles.

slide16
Биосенсоры на основе УОНТ

Биосовместимость нанотрубок

Присоединение к нанотрубке распознающей биомолекулы

Нанотрубки в жгутах

Индивидуальные нанотрубки

Расщепление жгутов,

получение индивид. нанотрубок

и удержание их от слипания

Использование жгутов

из нанотрубок

Биосовместимость

нанотрубок

Улучшение характеристик созданного ранее устройств

Биосовместимость

нанотрубок

Присоединение к нанотрубке

распознающей биомолекулы

Присоединение к нанотрубке

распознающей биомолекулы

Создание функционального устройства

slide17
Изучены особенности адсорбции органических молекул на поверхность одностенной углеродной нанотрубки

Расщепление жгутов нанотрубок

Ультразвук

Molecular Phys.(2003)

Изучено взаимодействие между молекулами пирен, нафталин и углеродной нанотрубкой в пленках. Определены структуры этих гибридов и рассчитана энергия взаимодействия. Показано, что для плоских π-сопряженных молекул величина их взаимодействия с нанотрубкой в значительной степени определяется соотношением площади молекулы и диаметром нанотрубки

biofunctionalization of carbon nanotube by dna

Biofunctionalization of carbon nanotube by DNA

Single-stranded biopolymer

DNA wraping, R. Smalley et al. CPL, 2001

Zheng et al. Nature, 2003

computer sumulation of swnt ssdna hybrid
Computer sumulation of SWNT:ssDNA hybrid

Hydrophilic

Hydrophobic

The single-stranded DNA chain forms a helical wrapping around the nanotube at which the nitrogen bases are extended from the backbone and stack onto the nanotube while the hydrophilic sugar-phosphate backbone turns to water.

computer sumulation of swnt polya hybrid
Computer sumulation of SWNT:polyA hybrid

Molecular dynamic simulation demonstrates that more than half of adenines is out of stacking with the tube surface and some of them can form self-stacking structuresFrom 30-nucleotides:

12 adenines were in - stacking with the nanotube surface,

7 bases formed self-stacking (two dimers and one trimer) and other adenines were out of stacking with SWNT surface

For simulation the program package NAMD was employed with Charmm27 force field parameter set. During simulation a box was applied, being of 55×55×135 Å dimensions in which poly(rA)-wrapped SWNT was embedded in water (more than 9000 H2O molecules). For modeling, the periodical boundary conditions were provided. SWNT was selected as a zigzag (16.0) carbon nanotube. Its length and diameter were 11.0 nm and 1.27 nm, respectively. The 30-nucleotides length of poly(rA) was selected for oursimulation.

V.A. Karachevtsev,et al (Chemical Physics &Physical Chemistry, 9, 2010 (2008)

calculation stacking energy interaction a a a swnt
Calculationstacking energy interaction A-A, A-SWNT

The interaction energy in the complex formed by adenine with a zigzag(10,0) SWCNT is -57 kJ/mol (calculated at the MP2/6-311++G(2d,p) level of theory).

Ab initio calculated stacking energy of adenines dimer is not more than -37 kJ/mol.

J. Sponer, J. Leszczynski, P. Hobza, Biopolymers 2002, 61, 3–31.

Stepanian et al J. Phys. Chem. A, 2009, 113 (15), 3621

slide24
Многослойное навивание ДНК вокруг нанотрубки

Karachevtsev et al. J. Nanoscience and

Nanotechnology (2008)

Компютерноемоделирование показало, чтотакиегибридыстабильны и удержаниеверхнихслоев ДНК над нижнимиосуществляется за счетобразованияводородныхсвязеймеждуазотистымиоснованиямиизразных нитей и фосфатным остовом.

Показано, что сравнительно длинная однонитевая ДНК может навиваться в несколько слоев вокруг нанотрубки по типу веретена. Предложена физическая модель такого гибрида, выполнены оценки энергии взаимодействия между отдельными фрагментами полимера.

double stranded dna swnt hybrid
Double-stranded DNA:SWNT hybrid

ds- DNA is a quite rigid polymer

In this model the ds-DNA-SWNT hybrid will be weak hydrophilic

biofunctionalization of carbon nanotube by double stranded dna

Biofunctionalization of carbon nanotube by double-stranded DNA

Will double-stranded biopolymer form a hybrid with nanotube by wrapping and form stable aqueous suspension?

  • In our model of the formation of fds-DNA:SWNT hybrid we assume that at the beginning the denatured regions of the fragmented polymer wrap around the nanotube under sonication. The ss-polymer parts are highly flexible can wrap around nanotube surface.These polymer tails serve as “anchor” holding the ds-parts of DNA close to the nanotube. The ds-regions coming into the interaction with the SWNT surface further stabilize the complex holding the DNA nearest to the nanotube surface.

G. Gladchenko, M. Karachevtsev et. al. (2006) 104, 3193 Mol. Phys.

carbon nanotube dna sensor
Carbon Nanotube DNA Sensor

Detection of DNA Hybridization Using the Near-Infrared Band-Gap Fluorescence of Single-Walled Carbon Nanotubes

Nano Lett., Vol. 6, No. 8, 2006

Nano Lett. 2006, 6, 371–375

uv spectroscopy dna melting curve
UV-spectroscopy DNA: melting curve

The conformational state of the polymer adsorbed on carbon nanotube surface can be also controlled by UV absorption spectroscopy.

heat cycling of the swnt dna aqueous solution
Heat cyclingofthe SWNT:DNA aqueous solution

The SWNT:DNA aqueous solution heat cycling up to 900 C does not lead to polymer release from tube surface

slide31

Гібридизація двох полінуклеотидів на поверхні вуглецевих нанотрубок є дефектною

Енергія утворення пари аденін (rА)-урацил (rU) у воді ~ 19, а енергія взаємодії поли(rА)-НТ ~ 33 кДж/моль.

Адсорбція полімеру на поверхні нанотрубки перешкоджає утворенню комплементарної пари з водневими зв’язками.

Цей результат слід враховувати при

створені геносенсора на НТ.

Доведено, що гібридизація ДНК на поверхні одностінної вуглецевої нанотрубки є дефектною.

Це пояснюється більшою енергією адсорбції полімеру на поверхні нанотрубки у порівнянні з

енергією утворення водневих зв’язків між азотними основами двох полімерів.

В.О. Карачевцев, Г.О. Гладченко, М.В. Карачевцев, В.С. Леонтьєв, В.О. Валєєв, О.C. Литвин (Chemical Physics &Physical Chemistry, 9, 2010 (2008))

polymer hybridization occurs with defects
Polymer hybridization occurs with defects

poly(rU) hybridization with poly(rA)NT occurs with defects along the whole polymer length because of π-π stacking between nitrogen bases and the nanotube surface, which hinders the usual hybridization process

Karachevtsev et al. ChemPhysChem 2008, 9, 2010 – 2018

slide33

SWNT emission

(9,2)

(9,2)

(10,2)

(14,0)

(7,5)

(9,4)

(11,3)

(9,4)

(6,5)

(11,4)

. For the semiconducting nanotubes their bandgap energy Eg is equal to the energy difference E11(dt) between the two van Hove singularities, the first subband edges of the valence and conduction bands.

Emission bands are correspond to individual semiconducting nanotubes of different diameters

Luminescence was excited by DPSS green laser at λex=532 nm.

Quantum yield is 10-3

glucose sensor based on the following biochemical reactions
Glucose sensor based on the following biochemical reactions:

Detection of the influence of the electron (product of reaction) on the nanotubes luminescence intensity is the main idea of the sensor.

near infrared optical sensors based on single walled carbon nanotubes
Near-infrared optical sensors based on single-walled carbon nanotubes

M.S. Strano et al. Nature materials, 4 (2005), 86.

The enzyme was immobilizeddirectly on the nanotube.

t he problem of enzyme immobilization on nanotube and of keeping its native activity
The problem of enzyme immobilization on nanotube and of keeping its native activity

It was shown recentlythat the activity of two enzymes: R-chymotrypsin and soybean peroxidase decreased significantly after their adsorption onto the surface of single-walled carbon nanotubes.

Soybean peroxidase retained up to 30% of its native activity upon adsorption while the adsorbed R-chymotrypsin retained only 1% of its native activity.[S.S. Karajanagi, A.A. Vertegel, R.S. Kane, and J.S. Dordick. Langmuir; 20(26); 2004, p.11594].

DNA polymerase decreases activity after adsorption onto carbon nanotubes surface (Changqing Yi et al. Nanotechnology 18 (2007) 025102).

Thus, the problem of enzyme immobilization on the nanotube and of keeping its native activity is the key feature

that should be investigated and understood before the work on the development of biosensors is carried out.

Our approach:

indirect immobilization of enzyme (GOX) on SWNTs with preservation of its activity which implies using the polymer as an interlayer between them. The DNA wrapped around the nanotube is an interlayer/interface between the enzyme and SWNT surface.

Karachevtsev et. al. CPL 435, 104 (2007).

afm image of swnt dna gox bionanohybrids
AFM image of SWNT:DNA:GOX bionanohybrids

The wire-like structure is associated with individual nanotubes around which single-stranded DNA was wrapped, and the distinct globular structures on the SWNT represent GOX molecules.

AFM image cross-section analysis along the nanotube or enzyme revealed that the height of globular structures above SWNTs ranges from 4.7 to 5.4 nm and also indicates that enzymes are adsorbed on DNA wrapped around the tube.

bionanihybrid swnt dna gox molecular dynamic modeling
BIONANIHYBRIDSWNT:DNA:GOX – molecular dynamic modeling

NAMD program

Box: 94.77×80.66×95.54 Å 19550 H2O molecules

For modeling the periodical boundary conditions were provided. In all the cases SWNT was selected as a zigzag (10.0) carbon nanotube. Its length and diameter were 5.1 and 0.796 nm, respectively. Polynucleotide used in the simulations were 15-nucleotides polyC.

Karachevtsev et. al. (2007) SPIE Proceed.

bionanihybrid swnt dna gox molecular dynamic modeling1
BIONANIHYBRIDSWNT:DNA:GOX – molecular dynamic modeling

Analysis of GOX and DNA interaction showed the availability of some molecular contacts, including H-bonds between some groups of amino acids that form the enzyme shell and DNA components. For example, we observed the formation of H-bond between oxygen of DNA phosphate group and OH group of tyrosine (left insert), between NH2 group of cytosine and CO group of glutamine (right insert) or asparagines.

slide40
High energy part of NIR luminescence spectra of carbon nanotubes in aqueous solution with DNA and DNA:GOX

In the nanotube emission spectrum after GOX adding a small spectral blue shift (not above 28 cm-1) was observed after GOX immobilization close to the tube. A blue shift in the spectrum of nanotube emission is observed after expanding the tube surface covering with the polymer due to decreasing an area of the nanotube hydrophobic contact surface with water

Luminescence was excited by DPSS green laser at λex=532 nm.

influence of glucose on intensity of nanotubes emission
Influence of glucose on intensity of nanotubes emission

Figure demonstrates the glucose injections influence on the nanotube luminescence intensity. We controlled the integral intensity of the most intensive band in the emission spectrum at 10070 cm-1, corresponding to the (6,5) nanotube index chirality. Two first glucose injections (1 mM each portion) decrease significantly the luminescence intensity but after each adding the percent of diminution of the intensity.

Karachevtsev et. al. (2007) SPIE Proceed.

conclusions

Conclusions

We have demonstrated a new approach for the indirect immobilization of the enzyme on SWNTs with keeping the enzyme activity. DNA wrapped around the nanotube is acting as interlayer/interface between the enzyme and nanotube surface.

DNA interacts effectively with the enzyme shell due to H-bonding between enzyme components and serves as an anchorage for GOX.

Such a method for enzyme immobilization onto a nanotube surface can be used in designing biosensors for glucose, lactate and others.

acknowledgments

ACKNOWLEDGMENTS

Dr. U. Dettlaff-Weglikowska, Stuttgart, Germany, for SWNTs purification

Dr. O.S. Lytvyn – Atom Force Microscopy study (ISP, Kyiv, Ukraine)

ILTPE, Kharkov, Ukraine:

Dr. G. Gladchenko – UV absorption spectroscopy

A. Yu. Glamazda –luminescence study

Dr. S. Stepanian and M.V. Karachevtsev – computer sumulation

V.S. Leontiev – biochemistry samples manipulations