Question: Next Generation Sequencing (NSG): There are 3 billion base pairs in a human DNA sequence, and tha…

Next Generation Sequencing (NSG): There are 3 billion base pairs
in a human DNA sequence, and that you have 50 copies of identical
full DNA molecules. Next, assume that you will use enzymes to break
the full DNA molecule into sections that can be anywhere between 80
and 120 base pairs in length. As a result, the location of enzyme
chopping (called enzyme cleavage) is not necessarily the same on
all 1000 DNA copies, but that on average, the base pair length is
100. The Illumina’s sensor chip has 8 channels, and each channel is
~ 60 mm long, 1 mm wide, where both the top and bottom are active
(usable) surfaces. We wish to distribute the DNA fragments of a
full human DNA molecule onto the chip. Assume that each fragment
must attach to a distinct location on the chip, and not overlap
with any of its neighbors. The size of a single Illumina “polony”
is estimated to be 24 µm2 .

(a) The laser used in the Illumina imaging system is capable of
delivering 100 mW of total power at 632 nm. The laser illumination
is shaped into a line that is 1 micron wide and 1 mm long, so it
can be scanned down the length of the channel (illuminating one
channel at once). Consider detection of the “G”-nucleotides and
each DNA fragment is labeled with only one Cy5 molecule with the
emission wavelength at 690 nm. Assume that the quantum efficiency
(or quantum yield) for Cy5 is 28% and that the fluorescence
emission is gathered by a lens with a focal length of 2.9 mm and a
numerical aperture (NA) of 0.85. How many photons/sec from the
laser reach one polony area? Assuming a laser line scan rate of 1
cm/sec, how many photons are emitted by one polony?