Electronic Supplementary Information

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1 Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 215 Electronic Supplementary Information An Upconversion Nanoprobe Operating in the First Biological Window Qiang Ju, Xian Chen, Fujin Ai, Dengfeng Peng, Xudong Lin, Wei Kong, Peng Shi, Guangyu Zhu, and Feng Wang* 1 3 Absorption coefficient (cm -1 ) oxyhemoglobin water deoxyhemoglobin Wavelength (nm) Figure S1. The absorption spectra of hemoglobin and water in the spectral range of 25 to 1 nm. (Prahl, S., Optical Absorption of Hemoglobin, Hale, G. M. et al., Appl. Opt. 1973, 12, 555.)

2 Figure S2. TEM images of a) NaYbF 4 :Nd (45 mol %) andd b) NaYbFF 4 :Er (2 mol %) nanoparticles prepared by the same protocol. A high Yb 3+ content in the host lattice results in very big particles, which limits their use for optical tuning and biolabeling studies Intensity (a.u.) NaYbF 4 :Nd@NaGdF 4 :Yb/Er@NaG GdF 4 core-shell-shell nanoparticles 2 NaGd.1 Yb.64 Er.1 Nd.25 F core-shell nanoparticles F 4 x Wavelength (nm) 65 7 Figure S3. A comparision of the emission spectra of NaYbFF 4 :Nd@NaGdF 4 :Yb/Er@ NaGdF 4 core shell shelll nanoparticles and NaGd.1 Yb.64Er.1 Ndd.25 F 4 core shell nanoparticles. The homogenerous dopedd nanoparticles display significantly suppressed optical emissions due to deleterious cross-relaxations between the dopant ions.

3 Figure S4. TEM images off the NaYbF 4 :Nd@NaGdF 4 :Yb/Er@NaGdF 4 core shell shell nanoparticles as a function of Yb 3+ concentration inn the inner shell s layer: a) 18%, b) 38%, and c) 58%. The scale bars are 1 nm. Alongg with the TEM image of NaYbF 4 :Nd@NaGdF 4 :Yb/Er@NaGdF 4 comprising 78% Yb in the inner shell layer (Figure 2d), these core shell shell nanopartilcess show veryy consistent size and morphology despite the largely different dopant concentrations of Yb 3+. Figure S5. TEM imagess of a) NaYbF 4 :Nd core, b) NaYbF 4 :Nd@NaYbF 4 :Er (2 mol %) core shell, and c) NaYbF 4 :Nd@NaYbF 4 :Er (2 mol %)@NaYF 4 core shell shell nanoparticles. In comparison with Figure 2c, the e NaYbF 4 shell s grown in the absence of the Gd 3+ cofactor were rather nonuniform, n, which impede precise control over energy transfer in the nanoparticles with high emission efficiency.

4 Figure S6. a) Proposed energy transfer mechanism at high ErE 3+ dopingg concentrations under the excitation at 888 nm. b) The emission spectra of NaYbFN 4 :Nd@ d@nagdf 4 : Yb/ 4 core shell shell upconversion nanoparticle es as a function of Er 3+ concentrations in the inner-shell. The e Yb 3+ concentration was fixed at 2 mol %.

5 1 OA-capped Transmittance (%) PAA-capped 1738 AEP-capped FA-conjugated Wavenumber (cm -1 ) Figure S7. FT-IR spectra of the as-synthesized core shell shell nanoparticles as well as the surface-modified counterparts. Additional IR band centered at 1738 and 1645 cm -1 were clearly observed after the ligand exchange reaction with PAA and AEP, which can be attributed to the C=O stretching mode of protonated carboxylate groups (-COOH) in PAA and the N-H bending mode of amino group in AEP, respectively. The results indicated the successful replacement of AEP and PAA for oleate ligands on the surfaces of the core shell shell nanoparticles. For the folic acid (FA)-conjuaged nanoparticles, a band peaked at 1686 cm -1 was observed due to the C=O streching mode of amide group, confirming the successful conjugation of FA to the AEP-capped nanoparticles.

6 Figure S8. Optical micrographs of PAA-capped nanoparticles after incubation with KB cells (1 μg/ml) for 4 hrs. a) Bright-field image that outlines thee profiles off the cells (Scale bar = 5 μm), b) DAPI blue images (λλ em = nm, λ ex x = 365 nm) that indicate the nuclear regions, c) Upconversion luminescence imaging (λ em = nm, λ ex = 88 nm) show the absence of non-specific binding. Figure S9. TEM images of a) NaYF 4 :Yb/Er (18/2 mol m %) core and b) the corresponding NaYF 4 :Yb/Er (18/2 mol %)@NaYF 4 core shell nanoparticles, which were used in this work for comparison. c) Emission spectrum of thee NaYF 4 :Yb/Er (18/2 mol %)@NaYF 4 core shell nanoparticles obtained byy excitationn with a 976-nm diode laser.

7 Figure S1. TEM images of a) PAA-capped and b) DNA-conjugated PAA-capped core shell shell nanoparticles, showing that the surface modification essentially does not alter the size and morphology of the as-synthesized nanoparticles. The scale bar is 5 nm. 6 Absorption o (a.u.) DNA-conjugated nanoparticles Nanoparticles Wavelength (nm) Figure S11. UV-Vis spectra of the DNA-conjugated nanoparticles and PAA-capped nanopartilces in PBS. The absorption band centered at 258 nm for the DNA-conjugated nanoparticles confirmed the successful linkage of DNA with the nanoparticles.

8 25 Intensity (a.u.) Wavelength (nm) Figure S12. The absorption (pink dotted line) and emission (blue dotted line) band of Cy5, as well as the red emission band of Er 3+ (red solid line). The reasonable overlap between the absorption of Cy5 and the emission of Er 3+ promises the energy transfer between nanoparticle and dye when they are in close proximity..1 Intensity Wavelength (nm) Figure S13. The enlarged upconversion spectra for the detection of target DNA of varying concentration (nm) in the far-red spectral region (68-71 nm) under 88 nm excitaion. A gradully increased emission of Cy5 was observed with the addition of increasing amount of target DNA, confirming the occurence of LRET.

9 Figure S14. a) Schematic illustrationn of the control experiment by using upconversion nanoparticles that were not conjugated with capture-dnaa as the energy donor. b) Upconversion spectra forr control experiments in the presence of target DNA of varying concentration. The essentially unaffected red emission intensity indicatess the absence of LRET because the distatnce between the nanoparticle donor and dye acceptor was enssentially unchanged.. Intensity (a.u.) Target DNA Target DNA mixed with random DNA only random DNA Target DNA mixed with BSA Wavelength (nm) 7 Figure S15. The emission spectra off the DNA-sensor random DNA sequences (red line), mixture of in the presence e of target-dna (black line), mixture of target DNA and target DNA and BSA (green line) and only randomm DNA (blue line). The concentration of target-dna is 3 nm, and the employed random DNAA sequencess are 5 -ATT TTG TCT GAA ACC ATG T-3 (1 nm), 5 -ACA TAA AGA AAT CAT GG-3 (1 nm) ), 5 -AGT TAA AGAA AAT CAT GGA AGT A AA-3 (1 nm). The emission intensity ratio in the presence of pure target-dna was.96, which iss not affected by the interference DNA of random sequences as well the presence of BSA. Under the same experimental conditions, no noticeable variation in emission intensity was detected in the absence of target-dna, further confirming high selectivity of the DNA-sensor.

10 1 Target DNA Single-base mismatched d target DNAA 8 Intensity (%) Concentr ration of Formamid de (v/v) Figure S16. A comparison of the sensor response to target-dna target t DNAA (5 -CAG CAT GAG TTT CTG AAA CC CC T- 3 ) at various formamide concentrations. (5 -CAG CAT CAG TTTT CTG AAAA CCC T- 3 ) and single-base mismatched Figure S17. a, b) DNA detection with the 98 nm-excited core shell c nanoparticles in a standard in vitro assay format and inn the presence of tissuee interference, respectively. The circlets in the calibration curves are variations in intensity of the relevant emission peaks in the presence of thee analyte. Error bars shown represent the standard deviations from five repeated measurements. c) The effectt of pork muscle tissue on attenuating the laser radiations of 888 and 98 nm, respectively.