Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection
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Surface Enhanced Raman as Tool to study Drug Protein Interactions and Nucleic Acid Detection. Chandrabhas Narayana (BHAS) Chemistry and Physics of Materials Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India [email protected]

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Surface Enhanced Raman as Tool to study Drug Protein Interactions and Nucleic Acid Detection

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Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

Surface Enhanced Raman as Tool to study Drug Protein Interactions and Nucleic Acid Detection

ChandrabhasNarayana (BHAS)

Chemistry and Physics of Materials

Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India

[email protected]

http://www.jncasr.ac.in/cbhas

ICPC Nanonet Webinar from JNCASR Campus on April 14, 2011


What happens when light falls on a material

What happens when light falls on a material?

Transmission

Reflection

Absorption

Luminescence

Elastic Scattering

Inelastic Scattering


Why are sky and sea blue

Why are Sky and Sea Blue?


Vibrations in molecules

Vibrations in Molecules

Sym. Stretching

8086 cm-1 = 1 eV

Room Temp = 25 meV

HCl

n = 2991 cm-1

HF

n = 4139 cm-1

Sym. Bending

H2O

Asym. Stretching

n1 = 3835 cm-1

n3 = 3939 cm-1

n2 = 1648 cm-1

Asym. Bending

NH3

n1 = 3505.7 cm-1

n4 = 1689.7 cm-1

n3 = 3573.1 cm-1

n2 = 1022 cm-1

SF6

n5 = 643.35 cm-1

n2 = 615.02 cm-1

n6 = 348.08 cm-1

n3 = 947.98 cm-1

n4 = 523.56 cm-1

n1 = 774.55 cm-1


Classical picture of raman

Classical Picture of Raman

Induced Polarization

Polarizability

Taylor Expansion

Stokes Raman

Anti-Stokes Raman


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

S

<eg,p2|Her|p2,eb> <eb,p2|Hep|p1,ea> <ea,p1|Her|p1,eg>

|Es-Eb|x|Ei-Ea|

a,b

Energy diagram and Quantum picture

Virtual states

Raman cross section

photon

ex

g

Electronic states

Vibrational states

If Ei = Ea or Es =Eb

We have Resonance Raman effect


Raman spectra of ccl 4

Raman spectra of CCl4

Isotope effect

Cl has two isotopes 35Cl and 37Cl

Relative abundance is 3:1


Raman fluorescence and ir

Raman, Fluorescence and IR

Absorption

and emission

Scattering

Absorption


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

  • Problems with Raman:

  • Very Weak – for every 109 photons only 1

  • photon Raman

  • Resonant Raman not feasible with every sample.

  • Absorption a better process than scattering


Origin of surface enhanced raman spectroscopy

Origin of Surface Enhanced Raman Spectroscopy

  • Initially – thought to be depended on Surface Area of the rough surface

  • It was shown that the scattering cross section far exceeded the number of molecules on the rough surface.

  • It was proposed that the origin was due to surface plasmons – hence a truly nano phenomenon.

  • Alkali and Ag the best, Au and Cu the next best, Al, In, Pt followed by transition metals and then bad conductors.

  • Exciting wavelength, polarization, exact nature of the nanostructure also effect the SERS


Plasmons in nanoparticles

Plasmons in Nanoparticles


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

Surface Enhanced Raman Scattering (SERS)Raman signal intensity gets enhanced when molecules are adsorbed on metal nanoparticles, colloids, island films etc.

  • Pathways for enhancement :

  • Electromagnetic enhancement

  • Enhanced local optical fields of metallic nanostructure

  • Chemical enhancement

  • Molecule-nanostructure system provide new energy states


Raman spectrometers

Raman Spectrometers


Drug protein interaction studies using sers

Drug Protein Interaction studies using SERS

With Tapas Kundu, JNCASR

Soumik Sidhanth, Partha Kundu

Pavan Kumar G V


The dynamic chromatin

+ H1

- H1

The Dynamic Chromatin

Transcriptional inactive

Transcriptional active

Hizume et al, Biochemistry, 2005, 44, p12978

Kundu and Takeyasu, 2005


Factors influencing transcriptional competence

Factors Influencing Transcriptional Competence

p300

CBP

GCN5

Ash1

CARM1

PRMT1

SWI/SNF

Rsc

NURF

HMG’s

Asf1

CAF1

Spt16

NPM1

SuV39A

Dot1

G9a

HDAC1

HDAC4

SIRT1

NuRD

HP1

MeCP2

PARP1

PC4


Sers of p300

G.V. Pavan Kumar et al. J. Phys. Chem. B (2006) 110, 16787.

Amide I

SERS of p300

Tyr and/or Phe

at 10 nM concentration

Tyr

Amide II

n(COO-)

Amide I

A III

A II

b - sheet

a - Helix


Hat modulators

S.No.

HAT modulator

Target

Reference

1

Lysyl-CoA

p300

Lau et al., 2000

2

H3-CoA-20

PCAF

Lau et al., 2000

Anacardic acid

3

Anacardic acid

p300/PCAF/CBP

Balasubramanyam et al., 2003

4

CTPB (activator)

p300

Balasubramanyam et al., 2003

5

Garcinol

p300/PCAF/CBP

Balasubramanyam et al., 2004

6

Curcumin

p300/CBP

Balasubramanyam et al., 2004

7

g-butyrolactones

CBP/Gcn5

Biel et al., 2004

8

Isothiazolones

p300/PCAF

Stimson et al., 2005

HAT modulators


Activity

C

DMSO

200mM

250mM

150mM

100mM

10mM

50mM

Activity

CTPB

CTB

DMSO

150mM

200mM

250mM

100mM

50mM

10mM

150mM

200mM

250mM

100mM

DMSO

150mM

200mM

250mM

100mM

DMSO

50mM

10mM

50mM

10mM

CH

Coommassie

Autoradiogram

Mentalingu et al J. Phys. Chem. B 111, 4527 (2007)


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

Interaction studies

Mentalingu et al J. Phys. Chem. B 111, 4527 (2007)


Synthetic hat domain of p300

Synthetic HAT Domain of p300

Liu et al Nature 451, 846 (2008) (February 14, 2008)


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

B

A

6j

6s

CPM

6t

CH

6j

6s

6t

6u

6v

DMSO

DMSO

6j

6s

6t

6u

6v

CH

Coommassie

6u

Autoradiogram

6v

Mentalingu et al J. Phys. Chem. B 111, 4527 (2007)


Effect of hydrophobic functional group

Effect of hydrophobic functional group

Mentalingu et al J. Phys. Chem. B 111, 4527 (2007)


Non pcr based detection of dna and rna using serrs

Non-PCR based detection of DNA and RNA using SERRS

With Udaykumar Ranga, JNCASR

Soumik Sidhanth, Gayathri K, Partha Kundu

Pavan Kumar G V


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

HIV STRAINS

HIV-1

HIV-2

M

N

O

A

B

C

D

E

J

A

B

C

D

---

to

---

Viral subtypes

99% (India)

13%56% (Global)


Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

AE

AG

AB

AGH

KU

HIV-1 recombinant viruses are growing at an alarmingly faster ratehttp://hiv-web.lanl.gov/content/hiv-db/CRFs/CRFs.html

  • In 2001 only 8 recombinants

  • In 2004, 16 recombinants

  • Today there are 34 CRFs


Strategies to detect recombinant viruses

Strategies to detect recombinant viruses

  • Sequencing the whole virus

    • Golden standard

    • Universal application: useful for all the known and emerging viruses

    • Technically demanding

    • Expensive

    • Doesn’t lend for automation

  • Multi-probe hybridization assay

    • A real-time PCR based technique

    • Expensive: several TaqMan probes required

    • Limited application: Useful for detecting 2 or 3 subtypes

    • False positive results (especially in sub-optimal conditions)


  • Schematic representation of hiv viral rna detection

    Schematic Representation of HIV Viral RNA Detection

    1 2 3 4 5 6 7 8 9 10

    Indian Patent (2007), PCT (2007)


    Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

    Template molecules

    (ss DNA)

    Viral

    subtype

    1013

    1012

    1011

    1010

    C

    A

    B

    SERRS intensity

    Raman shift

    HIV-1 subtype-C capture probe detects only C, not A and B strains

    • Window-1 (LTR)

    • Subtype-C capture probe (N 730c)

    • Acquisition time 1 sec

    • Assay sensitivity approx. 102 molecules


    Checking for b virus

    B-virus

    Capture

    probe

    B

    C

    Checking for B Virus

    Indian Patent (2007), PCT (2007)


    Gold coated magnetite nanoparticles

    Gold coated magnetite nanoparticles

    Superparamagneticbehaviour of gold coated magnetite nanoparticles


    Surface enhanced raman as tool to study drug protein interactions and nucleic acid detection

    SERS of R6G from detector probe after hybridization and washing


    Conclusions

    Conclusions

    • Raman provides information from the materials where all others fail.

    • Raman is going to strongly influence research in Biology.

    • Nanoparticle synthesis and plasmon tuning is going to be very important.

    • With the great developments in ab initio calculations and use of Gaussian, Raman would provide both physics and chemistry of the materials.

    Thank you for your attention!!!


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