On the feasibility of using the intrinsic fluorescence of nucleotides for DNA sequencing.
There is presently a worldwide effort to increase the speed and decrease the cost of DNA sequencing as exemplified by the goal of the National Human Genome Research Institute (NHGRI) to sequence a human genome for under $1000. Several high throughput technologies are under development. Among these, single strand sequencing using exonuclease appear very promising. However, this approach requires complete labeling of at least two bases at a time, with extrinsic high quantum yield probes. This is necessary because nucleotides absorb in the deep ultraviolet (UV) and emit with extremely low quantum yields. Hence intrinsic emission from DNA and nucleotides is not being exploited for DNA sequencing. In the present paper we consider the possibility of identifying single nucleotides using their intrinsic emission. We used the finite-difference time-domain (FDTD) method to calculate the effects of aluminum nanoparticles on nearby fluorophores that emit in the UV. We find that the radiated power of UV fluorophores is significantly increased when they are in close proximity to aluminum nanostructures. We show that there will be increased localized excitation near aluminum particles at wavelengths used to excite intrinsic nucleotide emission. Using FDTD simulation we show that a typical DNA base when coupled to appropriate aluminum nanostructures leads to highly directional emission. Additionally we present experimental results showing that a thin film of nucleotides show enhanced emission when in close proximity to aluminum nanostructures. Finally we provide Monte Carlo simulations that predict high levels of base calling accuracy for an assumed number of photons that is derived from the emission spectra of the intrinsic fluorescence of the bases. Our results suggest that single nucleotides can be detected and identified using aluminum nanostructures that enhance their intrinsic emission. This capability would be valuable for the ongoing efforts toward the $1000 genome.
- Research Organization:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Organization:
- National Institutes of Health (NIH); USDOE Office of Science (SC)
- DOE Contract Number:
- DE-AC02-06CH11357
- OSTI ID:
- 982670
- Report Number(s):
- ANL/CNM/JA-66029; TRN: US1005357
- Journal Information:
- J. Phys. Chem. C, Vol. 114, Issue 16 ; Apr. 29, 2010
- Country of Publication:
- United States
- Language:
- ENGLISH
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Related Subjects
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ACCURACY
ALUMINIUM
BASES
COST
DNA
DNA SEQUENCING
EMISSION
EMISSION SPECTRA
EXCITATION
FLUORESCENCE
HUMAN POPULATIONS
LEVELS
NANOSTRUCTURES
NUCLEOTIDES
PARTICLES
PHOTONS
POWER
SIMULATION
THIN FILMS