In order to answer this question the following experiment was carried out.

Firstly, we prepared 100 mM stock solutions in DMSO of cyanine dyes: Cyanine3, Sulfo-Cyanine3Cyanine5Sulfo-Cyanine5 NHS esters.

For comparison purposes we also prepared 100 mM stock solutions in DMSO of boron-dipyrromethene dyes: BDP TMR and BDP 630/650 NHS esters that have similar fluorescence spectrum with Cyanine3 and Cyanine5 NHS esters, respectively.

Secondly, 5 µM solutions of NHS esters were prepared by diluting the stock solutions with mQ water.

Finally, 1 ml of received 5 µM solutions of NHS esters was mixed with 1 ml of buffer solutions in separate tubes (pH: 8.3 - sodium hydrocarbonate, 7.4, 6.2, 4.5, 3.5 - sodium phosphate).

Measurements of the fluorescence emission spectra were taken with Perkin Elmer LS-55™ fluorometer.

The fluorescence emission spectra of Cyanine3, Sulfo-Cyanine3, BDP TMR NHS esters.

As can be seen from the graphs and a figure, the fluorescence intensity (RFU) of the cyanine dyes Cyanine3 and Sulfo-Cyanine3  is independent of the pH and remains nearly constant (within the range 5%). Meanwhile, the fluorescence intensity (RFU) of BDP TMR fluorophore does depend on the pH level and decreases in acidic environment (see pH 3.5, 4.5).

*Due to the very high fluorescence intensity of BDP TMR fluorophore 5 µM BDP TMR NHS ester solution was diluted 10-fold to a concentration of 0.5 µM to avoid exceeding the instrument measuring range. For the same reason we don’t see changes in brightness of fluorescence in tubes with BDP TMR solution on the figure.

Fluorescence emission spectrum of Cyanine3 depending on pHFluorescence emission spectrum of Sulpho-Cyanine3 depending on pHFluorescence emission spectrum of BDP TMR depending on pHVisible fluorescence of Cyanine3; Sulfo-Cyanine3; BDP TMR in tubes under UV light

The fluorescence emission spectra of Cyanine5, Sulfo-Cyanine5, BDP 630/650 NHS esters. 

Similarly, you can see from the graphs and a figure that the fluorescence intensity (RFU) of the cyanine dyes Cyanine5 and Sulfo-Cyanine5  is independent of the pH and remains nearly constant (within the range 5%). Meanwhile, the fluorescence intensity (RFU) of BDP 630/650 fluorophore does depend on the pH level and decreases in acidic environment (see pH 3.5, 4.5).

Fluorescence emission spectrum of Cyanine5 depending on pHFluorescence emission spectrum of Sulfo-Cyanine5 depending on pHFluorescence emission spectrum of BDP 630/650 depending on pHVisible fluorescence of Cyanine5; Sulfo-Cyanine5; BDP 630/650 in tubes under UV light
 

Summarizing all above-mentioned information we can conclude that the fluorescent intensity of the cyanine dyes: Cyanine3Sulfo-Cyanine3Cyanine5Sulfo-Cyanine5 NHS esters do not depend on the pH value and remain constant, but the fluorescent intensity of the boron-dipyrromethene dyes: BDP TMRBDP 630/650 NHS esters depend on  pH conditions and decreases significantly in acidic environment.

Perkin Elmer LS-55™ is trade mark of PerkinElmer.