Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer

Transcription

1 Triangulating Nucleic cid Conformations Using Multicolor Surface Energy Transfer Supporting Information Ryan. Riskowski 1, Rachel E. rmstrong 2, Nancy L. Greenbaum 3, Geoffrey F. Strouse 1,2 * 1 Molecular iophysics Program, Florida State University, Tallahassee, FL 32306, United States 2 Department of Chemistry and iochemistry, Florida State University, Tallahassee, FL United States 3Department of Chemistry and iochemistry, Hunter College and The Graduate Center of the City University of New York, New York, NY 10065, United States Supporting Information I. McSET Complex ssembly. Scenario I (Supporting Figure SF1). KCN Etch (Supporting Figure SF2, SF3) C. Scenario II (Supporting Figure SF4) II. Scattering Contribution to Lifetime Data (Supporting Figure SF5) III. FRET-Only and SET-Only data. bsorbance and Emission Spectra (Supporting Figure SF6). Scheme I Fluorescence Decay (Supporting Figure SF7) C. Scheme II Fluorescence Decay (Supporting Figure SF8) D. Hammerhead ribozyme FRET-Only and SET-Only Results (Supporting Table ST1, ST2) IV. Energy Transfer Calculations. Derivation of McSET Formula. Calculation of d 0 and R 0 C. Constants for SET and FRET Calculations (Supporting Table ST3, ST4) S1

2 I. Characterization of Nucleic cid Complex ssembly. Linear DN ssembly (Scenario I) Figure SF1: 1% garose Gel in 1x TE running buffer at 10V/cm, showing assembly of the linear DN construct used in Scenario I. Lane numbering from the left is the same in both images; Lane 1: unlabeled SPP-coated 10 nm u nanoparticles. Lane 2: unlabeled SPP-coated 10 nm unp mixed with unbound ROX and DyLt680-labeled dsdn. Lane 3: Fully assembled 10 nm unp covalently bound to ROX- and DyLt680-labeled dsdn. ) Reflected light image showing bands of gold nanoparticles. The reduced rate of mobility in the gel indicates gold nanoparticles covalently bound to DN. Smearing of the band is due to a distribution in label occupancy on the particle surface a. ) UV illuminated gel image showing dye-labeled DN. The presence of a clear DN band is indication of unattached DN. The lack of a clearly visible DN band in the covalently attached sample is the result of quenching by the unp and indicates very low levels of unbound DN. Image contrast enhanced in Microsoft PowerPoint. a Pellegrino, T.; Sperling, R..; livisatos,. P.; Parak, W. J. Gel Electrophoresis of Gold-DN Nanoconjugates. J iomed iotechnol (2007), 2007, S2

3 . Determining DN labeling efficiency by CN etching. Figure SF2: bsorbance data from KCN etch control studies of ) 10 nm unp only, and ) 10 nm unp attached to dye labeled dsdn. unp exhibits a transient absorbance that disappears within 40 minutes after addition of 80mM KCN. Labeling of individual traces is explained in each image. To avoid convolution with this transient absorbance, quantification of DN was made 1hr after KCN addition. unp etching in the presence of dye labeled DN leads to a consistent 23% decrease in absorbance for DyLt680, but ROX remains unchanged. bsorbance values were corrected for concentration. S3

4 Figure SF3: bsorbance data used to determine stoichiometry of DN duplex per unp in Scenario I. Strands per particle are determined from the ratio of DN/NP concentration as determined by extinction. Nanoparticle concentration is determined from the plasmon peak at 520 nm before CN etching, and DN concentration is determined from the dye label extinctions taken after CN etching. When using DyLt680 post-kcn absorbance to quantify labeling efficiency, corrections are made to account for the 23% decrease in absorbance. verage labeling efficiency was ~9 DN duplexes per particle. S4

5 C. RN Hammerhead Ribozyme ssembly (Scenario II) Figure SF4: UV illumination image of nondenaturing PGE in 1x TE running buffer at 10V/cm stained with Sybr Green following manufacturer s protocol showing assembly and catalytic competence of the Hammerhead RN construct used in Scenario II. In all lanes, Ribozyme consists of catalytic core annealed to Cy3-labeled substrate in 20mM PS at a 1:1.1 ratio of Substrate:RN catalytic core. Cleavage reactions were performed by incubating ribozyme in 100 mm Mg 2+ for 2 hours. Lane numbering from the left; Lane 1: unlabeled ribozyme. Lane 2: ribozyme bound to 2 nm u NP. Lane 3: F647 labeled ribozyme. Lane 4: fully labeled ribozyme. Lane 5: labeled substrate strand only. Lane 6: unlabeled ribozyme after incubation with Mg 2+. Lane 7: ribozyme bound to 2 nm unp after incubation with Mg 2+. Lane 8: F647 labeled ribozyme after incubation with Mg 2+. Lane 9: F647 labeled ribozyme bound to 2 nm unp after incubation with Mg 2+. NG = nano-gold particle. Image contrast enhanced in Microsoft PowerPoint. S5

6 II. Scattering Contribution to Lifetime Measurements C D E Figure SF5: 3D Streak-Camera decay profiles showing the time-dependent signal of the excitation pulse scattering from the 10 nm gold nanoparticles used in Scenario I. ll spectra were collected in 20 mm PS (ph 6.5) and were excited at 560 nm. ) Decay of free ROXlabeled DN. The scattering of the pulse from the sample cuvette is visible as a distinct and well-separated peak at 560 nm that is below detection after ~1 ns. ) Decay of the dual labeled dsdn FRET complex. s in panel, the excitation pulse is a well resolved peak at 560 nm and below detection after ~1 ns. C) Decay of ROX-labeled DN bound to 10nm unps. Scattering of S6

7 the excitation pulse from the gold particles can be seen as a much larger portion of the signal due to strong quenching of the ROX dye, and the pulse persists for >1 ns. D) Decay of duel labeled dsdn FRET complex bound to 10 nm unp. s in C, scattering of the excitation pulse from the gold particles comprises a much larger portion of the signal due to strong quenching of the ROX dye, and the pulse can be seen to persist for longer than 1 ns. E) Collected scattering signal from a sample containing free 10 nm unps only. The broadened scattering signal can be clearly distinguished and the persistence of the signal out to ~2 ns can be seen. IIII. FRET-Only and SET-Only data. bsorbance and Emission Spectra Scenario I Scenario II Figure SF6: ) Normalized absorbance of 10 nm unp overlapped with emission and absorbance profiles of ROX and DyLt680 dye labels. ) Normalized absorbance of 2 nm unp overlapped with emission and absorbance profiles of Cy3 and F647 labels.. Scenario I DN FRET and SET Decays Figure SF7: ) Normalized fluorescence decay of ROX undergoing FRET on the dsdn ROX-DyLt680 complex in the absence of 10 nm unp. ) Normalized fluorescence decay of ROX undergoing SET on a dsdn strand labeled only with ROX and 10nm u (no DyLt680). Excitation was at 560 nm. S7

8 C. Scenario II - Hammerhead RN FRET and SET Decays Figure SF8: ) Normalized fluorescence decay of Cy3 undergoing FRET on the F647 labeled Hammerhead ribozyme complex annealed to a Cy3-labeled substrate in the absence of unp. ) Normalized fluorescence decay of Cy3 undergoing SET on a Hammerhead complex labeled only with Cy3-substrate and 2 nm u labeled ribozyme (no F647). D. Hammerhead RN FRET and SET Results Table ST1: Experimental and theoretical values for constructs undergoing SET only (no FRET). Dashes are used as entries when the corresponding data are not applicable. Here DyLt680 is not acting as a SET donor, and so does not experience any experimentally measured quenching value. It is only possible to set a lower bound for the distance between DyLt680 and unp, such that the absence of measureable energy transfer places the dye label at >190 Å from the unp surface. Figure ST2: Experimental and theoretical values for constructs undergoing FRET only (no SET). S8

9 IV. Energy Transfer Calculations. Derivation of McSET Formula We begin with the assumption that SET (k S ) and FRET (k F ) rates remain unperturbed when multiplexed as designed. The observed efficiency of quenching for a multiplexed SET-FRET systems (E SF ) is defined as the ratio of combined energy transfer rates (k S + k F ) to the sum of all decay rates (k S + k F + 1 τ 0 ), where τ 0 is the donor lifetime in the absence of FRET or SET. Therefore: E SF = k S + k F k S + k F + 1 τ 0 1 = 1 + (τ 0 (k S + k F )) 1 (SE1) => (k S + k F ) = τ 1 0 (E 1 SF 1) 1 (SE2) Rearrangement yields the following relations: k S = τ 1 0 (E 1 SF 1) 1 k F k F = τ 1 0 (E 1 SF 1) 1 k S (SE3a) (SE3b) Then, remembering that 1 E S = 1 + (d d 0 ) 4 = k S 1 k S + τ 0 (SE4a) nd 1 E F = 1 + (R R 0 ) 6 = k F 1 k F + τ 0 (SE4b) we rearrange to retrieve: k S = τ 1 0 (d d 0 ) 4 (SE5a) k F = τ 1 0 (R R 0 ) 6 (SE5b) Inserting the relations from SE5 into SE3 yields: (d d 0 ) 4 = (E 1 SF 1) 1 (R R 0 ) 6 (SE6a) (R R 0 ) 6 = (E 1 SF 1) 1 (d d 0 ) 4 (SE6b) S9

10 Finally, recognizing that E 1 SF = (1 τ SF τ 0 ) 1 (SE7) => (E 1 SF 1) 1 = τ 0 τ SF 1 (SE8) we can now rearrange again to produce the final expressions: d = d 0 [( τ 0 τ 1) ( R 6 1/4 ) ] R 0 (SE9a) for the SET contact distances. nd R = R 0 [( τ 0 τ 1) ( d 4 1/6 ) ] d 0 (SE9b) for FRET contact distances.. Calculation of d 0 and R 0. For Surface Energy Transfer, calculations of d 0 values are obtained from previously reported approaches. d 0 = αλ (φ) 1/4 ( n r (1 + ε 2 1 n m 2n m ε 2 2)) 1/4 (SE10) The value d 0 is the distance at which the probability of energy transfer is 50%, in analogy to R 0 in FRET. The donor specific terms are: λ, the emission wavelength maximum for the donor, and Φ, the quantum yield of the donor. The acceptor specific terms include, the absorptivity of a gold nanoparticle; n r, the refractive index of the metal; and ε 2, the complex dielectric function of the metal which comprises real and imaginary components (ε 2 = ε 2 + i ε 2 ). bove, ε 1 is the solvent dielectric and n m is the index of refraction for the solvent. The orientation of the donor to the metal plasmon vector, α, is taken as the averaged orientation vector resulting in α = ((9/2) 1/4 )/4π. The -term in SE10 can be expressed in terms of the absorptivity within a single nanoparticle in analogy to molecular absorption, can be formulated as: np = 10 3 ln(10) [ λ (2 r cm ( 2 r cm δ skin )) N V cm 3 ] (SE11) S10

11 where λ is the extinction coefficient of the NP at the maximum emission wavelength of the donor (size dependent λ values are reported for spherical unps 33,34 ), r cm is the radius of the NP in cm, N is vogadro s number, and V cm 3 is the volume of the particle in cm 3. (2r cm /δ skin )is a correction term to account for the depth into the particle which the donor electric field can penetrate. For FRET, calculations of R 0 are obtained using the well-known FRET equations. R 0 = [κ 2 n 4 φ 0 J ] 1/6 (SE12) nalogous to d 0 in SET, R 0 is the distance at which the probability of energy transfer is 50%. κ 2 is the orientation factor typically taken to be 2/3, n is the refractive index of the media, and φ is the quantum yield of the donor. The J-overlap integral, <J>, is obtained using the following integration: J = F D (λ)ε (λ)λ 4 dλ (SE13) F D (λ) is the emission of the donor normalized to an area of 1. ε (λ) is the molar absorptivity of the acceptor, and λ is wavelength in units of nm. The units of <J> in this formulation are cm 2 nm 4 /mol. C. Constants for SET and FRET calculations Table ST3: Values used in calculating d 0 and R 0 values for ROX and DyLt680 in Scenario I. Table ST4: Values used in calculating d 0 and R 0 values for Cy3 and F647 in Scenario II. S11