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Molecular Spectroscopy: Principles and Biophysical Applications BiCh132 Fall Quarter 2012 Jack Beauchamp. Many of the illustrations and tables used in these presentations were taken from the scientific literature and various WWW sites; the authors are collectively acknowledged.

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Molecular Spectroscopy: Principles and Biophysical Applications BiCh132 Fall Quarter 2012 Jack Beauchamp


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    1. Molecular Spectroscopy: Principles and Biophysical Applications BiCh132 Fall Quarter 2012 Jack Beauchamp Many of the illustrations and tables used in these presentations were taken from the scientific literature and various WWW sites; the authors are collectively acknowledged. This presentation is adapted in part from BiCh132 lectures of Professor Barton. Molecular Probes Handbook -11th Edition (Invitrogen) Recommended text: “Principles of Fluorescence Spectroscopy” by J. R. Lakowicz (3rd Edition; 2006)

    2. Introduction to Fluorescence Spectroscopy Useful probe of: environment structure dynamics chemical reactions Timescales: visible absorption~ 10-15 sec vibrations ~ 10-14 sec emission~ 10-9 sec for allowed transitions 10-6-10-3 sec for forbidden transitions On these timescales, emission is sensitive to competing processes

    3. Solvent Collisional vibrational dissipation ~ 10-12s S1 Intersystem crossing T1 Absorption 10-15 s Fluorescence 10-9 s Phosphorescence 10-6 – 10-3 s S0 Simplified Energy Level Diagram (Jablonski Diagram) 3 2 1 0 3 2 1 0

    4. Franck-Condon Principle for Electronic Transitions Franck–Condon principle energy diagram. Since electronic transitions are very fast compared with nuclear motions, vibrational levels are favored when they correspond to a minimal change in the nuclear coordinates. The potential wells are shown favoring transitions between v = 0 and v = 2.

    5. Franck-Condon Principle for Electronic Transitions Schematic representation of the absorption and fluorescence spectra corresponding to the energy diagram in previous slide. The symmetry is due to the equal shape of the ground and excited state potential wells. The narrow lines can usually only be observed in the spectra of dilute gases. The darker curves represent the inhomogeneous broadening of the same transitions as occurs in liquids and solids. Electronic transitions between the lowest vibrational levels of the electronic states (the 0-0 transition) have the same energy in both absorption and fluorescence.

    6. Franck-Condon Principle for Electronic Transitions (1926) Classically, the Franck–Condon principle is the approximation that an electronic transition is most likely to occur without changes in the positions of the nuclei in the molecular entity and its environment. The resulting state is called a Franck–Condon state, and the transition involved, a vertical transition. The quantum mechanical formulation of this principle is that the intensity of a vibronic transition is proportional to the square of the overlap integral between the vibrational wavefunctions of the two states that are involved in the transition. Edward Condon

    7. Edward Condon

    8. F =fluorescence quantum yield = fraction of singlets relaxing from excited state via fluorescence # photons emitted by fluorescence unless some catalytic chemiluminescent process Fluorescence Intensity x # excited state molecules x c I0 kF = rate of spontaneous emission P00 = transition probability same path for excitation and emission = # photons absorbed Rate constant for emission = kF + (rate constants for non-radiative pathways) Fluorescence Quantum Yields

    9. S1 kis T1 kF kic kq S0 What processes compete with fluorescence? 1. Internal conversion, kic collision with solvent dissipation of energy through internal vibrational modes basically transfer into excited vibrational states of S0 Note - kic increases with T therefore FF decreases with T

    10. 2. Intersystem crossing, kis spin exchange converts S to T get slow spin-forbidden phosphorescence for metal complexes often a mixture of states so “luminescence” 3. Collision with quencher, kq e.q. S1+Q S0+Q* molecules can quench excited state by: energy transfer spin exchange (paramagnetic + spin orbit coupling) electron transfer or proton transfer (+ energy) S1 kis T1 kF kic kq S0

    11. So, what matters are the rates of these competing processes Note - kF is not temperature dependent but all else is

    12. Decay Kinetics of S1 Suppose initially have concentration in S1 of S1(0) then turn off light Integrating, where fluorescence lifetime (measurable) If no other processes except fluorescence, then Radiative lifetime Also,

    13. Practical things: Sample Excitation Monochromator Emitted light Light source Emission Monochromator Detector Can measure steady state or time resolved emission For lifetimes: - then flash and turn off light and measure decay as a function of time - flash photolysis - single photon counting - streak cameras - time resolution depends on flash (also frequency domain measurements - phase modulation) For quantum yields, need geometry constant and correct for emission detectors -use standards (actinometry)

    14. Practical (sometimes annoying) things: Fluorescence Polarization / Depolarization Principle: When a fluorescent molecule is excited with plane polarized light, light is emitted in the same polarized plane, provided that the molecule remains stationary throughout the excited state (which has a duration of 4 nanoseconds for fluorescein). If the molecule rotates and tumbles out of this plane during the excited state, light is emitted in a different plane from the excitation light. If vertically polarized light is exciting the fluorophore, the intensity of the emitted light can be monitored in vertical and horizontal planes (degree of movement of emission intensity from vertical to horizontal plane is related to the mobility of the fluorescently labeled molecule). If a molecule is very large, little movement occurs during excitation and the emitted light remains highly polarized. If a molecule is small, rotation and tumbling is faster and the emitted light is depolarized relative to the excitation plane.

    15. Fluorescence Polarization / Depolarization Schematic representation of FP detection. Monochromatic light passes through a vertical polarizing filter and excites fluorescent molecules in the sample tube. Only those molecules that are oriented properly in the vertically polarized plane absorb light, become excited, and subsequently emit light. The emitted light is measured in both the horizontal and vertical planes.

    16. Fluorescence Polarization / Depolarization Here Ill is the intensity of emitted light polarized parallel to the excitation light, and I⊥ is the intensity of emitted light polarized perpendicular to the excitation light. An important property of the polarization that emerges from this equation is that it is independent of the fluorophore concentration. Although this equation assumes that the instrument has equal sensitivity for light in both the perpendicular and parallel orientations, in practice this is not the case.

    17. Sarah A. Weinreis, Jamie P. Ellis, and Silvia Cavagnero, Dynamic Fluorescence Depolarization: A Powerful Tool to Explore Protein Folding on the Ribosome, Methods. 2010 , 52(1): 57–73. doi:  10.1016/j.ymeth.2010.06.001

    18. Anne Gershensonand Lila M. Gierasch, Protein Folding in the Cell: Challenges and Progress, CurrOpinStruct Biol. 2011, 21(1):32–41. http://dx.doi.org/10.1016/j.sbi.2010.11.001 Schematic depiction of a protein folding reaction in the cytoplasm of an E. coli cell, showing vividly how different the environment is from dilute in vitro refolding experiments. The cytoplasmic components are present at their known concentrations. Features of particular importance to the folding of a protein of interest (in orange) are: the striking extent of volume exclusion due to macromolecular crowding, the presence of molecular chaperones that interact with nascent and incompletely folded proteins (GroEL in green, DnaK in red, and trigger factor in yellow), and the possibility of co-translational folding upon emergence of the polypeptide chain from the ribosome (ribosomal proteins are purple; all RNA is salmon). The cytoplasm image is courtesy of A. Elcock.

    19. Practical things (for a few $ more): http://www.olympusfluoview.com/applications/fretintro.html

    20. Stokes shift: fluorescent emission is red-shifted relative to absorption Excitation Spectrum – the excitation wavelength is scanned while the emission wavelength is held constant Emission Spectrum - the emission wavelength is scanned while the excitation wavelength is held constant - often gives the mirror image of the absorption spectrum Mirror generally holds because of similarity of the molecular structure and vibrational levels of S0 and S1 Given the Franck-Condon Principle, electronic transitions are vertical, that is they occur without change in nuclear positions. If a particular transition probability between 0 and 2 vibrational levels is highest in absorption, it will also be most probable in emission.

    21. Some Exceptions to Mirror Image Rule 1. Contaminants !! 2. Excitation to higher state(s) S2 3. Different geometry in excited state 4. Exciplexes (CT state) 5. Excimers 6. pK effects (excited state acid base properties) Dimer excited state

    22. Acid-base properties are modified in electronically excited states Example- pKa for acridine in ground state= 5.5 pKa for acridine in excited state= 10.7 protonation can occur during excited state lifetime Effects are quantified with use of the Förster Cycle Think of some applications of this phenomenon

    23. Förster Cycle: Quantifies changes in acid-base properties in electronically excited states ArOH (aryl alcohol such as napthol) – The shift in absorption spectra of the acid and its conjugate base can be used to quantify the difference in pKa in the ground and excited electronic state

    24. Fluorescent Probes Absorption and emission spectra of biomolecules. Top: Tryptophan emission from proteins. Middle: Spectra of extrinsic membrane probes. Bottom: Spectra of the naturally occurring fluorescence base, Yt base. DNA itself(---) displays very weak emission .

    25. Absorption Fluorescence Probe lmax max (x10-3) lmax F F (ns) Dansyl chloride 340-350 4.3 510-560 0.1-0.3 10-15 Ethidium 274 1.4 303 0.05 2 Normally use extrinsic probes or modified bases/ unnatural amino acids (check out the Molecular Probes Catalogue) + DNA ~1 20 when intercalated, yield and lifetime increase

    26. F1 Q F2 Fluorescence Quenching If you have 2 fluorescent components (probes), even two bound components, they will have different rates of quenching, kq kqfor F1 > kqfor F2 kq gives measure of accessibility of chromophore

    27. Stern-Volmer Analysis of Quenching In the absence of quencher, in the presence of quencher, where quenching is the result of bimolecular collisions.

    28. Stern-Volmer Plot Slope=KSV 1 [Q] Stern-Volmer quenching with concentration of Q, [Q] where KSV=kq

    29. Values of kq reflect collisional frequency and bimolecular diffusion controlled rate constant, k0 Smoluchowski eqn. R= collisional radii D= diffusion coefficients kq= fQk0 fQ = quenching efficiency if fQ= 0.5, 50% of collisions lead to quenching Can estimate D from Stokes-Einstein eqn. expect kq’s of 1010 M-1s-1 or less

    30. Consider equilibrium formation of a ground state complex which is not fluorescent: Q + F FQ The total conc. of fluorophore = or If FQ is not fluorescent, then fraction of fluorescence

    31. so that gives same KS.V. as Slope=KS.V. 1 [Q] [Q] But could have or even [Q] [Q]

    32. [Q] [Q] Dynamic Static For dynamicquenching, quenching process is diffusion controlled For staticquenching but no change in  – not a diffusion controlled process

    33. Singlet-Singlet Energy Transfer (Förster Transfer)

    34. Singlet-Singlet Energy Transfer (Förster Transfer)

    35. Singlet-Singlet Energy Transfer (Förster Transfer) Very useful for “long range” distance (20-80 Å) R R Donor Acceptor

    36. Pick donor and acceptor to have appropriately matched energy levels: D* A* kT= rate constant for transfer A0 kT D0 D* +A0 D0+A* k-T k-T is not likely given rapid vibrational relaxation Emission Absorption Absorption Emission A A D D Energy transfer gives sensitized emission and donor deexcitation Resonant interaction with acceptor excitation- weak coupling limit

    37. Real world example: Cyan fluorescent protein/Red fluorescent protein Absorption and emission spectra of cyan fluorescent protein (CFP, the donor) and red fluorescent protein (RFP or DsRed, the acceptor). Whenever the spectral overlap of the molecules is too great, the donor emission will be detected in the acceptor emission channel. The result is a high background signal that must be extracted from the weak acceptor fluorescence emission.

    38. What’s the basis for the interaction? -As in exciton coupling, dipole-dipole: just weak coupling limit Can describe the potential operator Where R is distance between A + D and are dipole moment operators lump all geometric and orientational parameters in here- really hard to know , lots of variability = 0-4

    39. According to Fermi’s Golden Rule: -rate of transition is proportional to the square of the expectation value for the interaction causing the excitation. for isoenergetic D(b a) emission A(a b) excitation emission absorption quantum yield lifetime of donor w/o acceptor frequency of transition extinction coefficient for A

    40. For general case, where transition involves a range of frequencies where refractive index of medium between donor and acceptor and normalized fluorescence of donor overlapping with acceptor or

    41. Naively, looks like D is emitting and A is reabsorbing but that transfer is trivial. Also what would be effect on ? Usual to define efficiency

    42. get 1/R6 dependence for E can measure 10-100 Å distance separations depending on FRET pair Want to measure donor-acceptor partners near R0 depending on experiment This yields largest change in E for small changes in R that occur in the given experiment.

    43. Very unique distance regime - FRET provides a spectroscopic ruler

    44. Selected Applications of FRET • Structure and conformation of proteins • Spatial distribution and assembly of protein complexes • Receptor/ligand interactions • Immunoassays • Probing interactions of single molecules • Structure and conformation of nucleic acids • Real-time PCR assays and SNP detection • Detection of nucleic acid hybridization • Primer-extension assays for detecting mutations • Automated DNA sequencing • Distribution and transport of lipids • Membrane fusion assays • Membrane potential sensing • Fluorogenic protease substrates • Indicators for cyclic AMP and zinc - Molecular Probes website

    45. Different ways to carry out experiment: monitor quenching of donor and/or enhanced emission by acceptor D alone D+A 1.) Quenching of donor I l E= fraction of donors deexcited therefore 1-E= fraction of donors remaining excited 2.) Enhanced emission by acceptor -should be sensitized emission: excite D, watch A emit D absorb I Acceptor emission l watch here

    46. In practice, want 3 replicas for study: Dalone D+A Aalone A sensitized emission donor quench An example: Distance measurement in melittin Depending upon solvent, can exist as monomer or tetramer, -helix or random coil

    47. Determine overlap integral for trp/dansyl pair: R0= 23.6 Å Overlap integral (shaded area) for energy transfer from a tryptophan donor to a dansyl acceptor on melittin. R0=23.6 Å

    48. E=0.45 R=24.4Å

    49. But there are issues- 1.) 2 is not known, nor directly measurable for so even rough estimate suffices Dale Eisinger Method- exploit the jitter macromolecule acceptor κ is related to the relative orientation of the donor/acceptor pair donor Likely there is fast geometric averaging before transfer, blurring 2 often set 2=2/3 for dynamic avg. of all geometries means uncertainty in R is < 15%