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

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? Interactions and Nucleic Acid Detection

Transmission

Reflection

Absorption

Luminescence

Elastic Scattering

Inelastic Scattering


Why are sky and sea blue
Why are Sky and Sea Blue? Interactions and Nucleic Acid Detection


Vibrations in molecules
Vibrations in Molecules Interactions and Nucleic Acid Detection

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 Interactions and Nucleic Acid Detection

Induced Polarization

Polarizability

Taylor Expansion

Stokes Raman

Anti-Stokes Raman


S Interactions and Nucleic Acid Detection

<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 CCl Interactions and Nucleic Acid Detection4

Isotope effect

Cl has two isotopes 35Cl and 37Cl

Relative abundance is 3:1


Raman fluorescence and ir
Raman, Fluorescence and IR Interactions and Nucleic Acid Detection

Absorption

and emission

Scattering

Absorption


  • Problems with Raman: Interactions and Nucleic Acid Detection

  • 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 Interactions and Nucleic Acid DetectionSurface 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 Interactions and Nucleic Acid Detection in Nanoparticles


Surface Enhanced Raman Scattering (SERS) Interactions and Nucleic Acid DetectionRaman 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 Interactions and Nucleic Acid Detection


Drug protein interaction studies using sers
Drug Protein Interaction studies using Interactions and Nucleic Acid DetectionSERS

With Tapas Kundu, JNCASR

Soumik Sidhanth, Partha Kundu

Pavan Kumar G V


The dynamic chromatin

+ H1 Interactions and Nucleic Acid Detection

- 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 Interactions and Nucleic Acid Detection

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. 16787.

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 16787.

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)


Interaction studies 16787.

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


Synthetic hat domain of p300
Synthetic HAT Domain of p300 16787.

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


B 16787.

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 16787.

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 16787. SERRS

With Udaykumar Ranga, JNCASR

Soumik Sidhanth, Gayathri K, Partha Kundu

Pavan Kumar G V


HIV STRAINS 16787.

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)


AE 16787.

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 16787.

  • 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 16787.

    1 2 3 4 5 6 7 8 9 10

    Indian Patent (2007), PCT (2007)


    Template molecules 16787.

    (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 16787.

    Capture

    probe

    B

    C

    Checking for B Virus

    Indian Patent (2007), PCT (2007)


    Gold coated magnetite nanoparticles
    Gold coated magnetite nanoparticles 16787.

    Superparamagneticbehaviour of gold coated magnetite nanoparticles



    Conclusions
    Conclusions washing

    • 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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