The removal of fluorescence in sequencing-by-synthesis

Double-layer focal plane microscopy for high throughput DNA sequencing

Throughput is one of the most important properties in DNA sequencing. We propose a novel double-layer focal plane microscopy that doubles the DNA sequencing throughput. Each fluorescence channel is divided into two tube lens channels by energy splitting, and the camera is adjusted to take images corresponding to different defocus positions of the objective, thus doubling the information capacity of the microscopy. The microscopy is applied to gene chip, which has high spatial frequency and good uniformity, so the simultaneous imaging of the two tubes has little influence on each other due to the spatial averaging effect. Experimental results show that the image signal to noise ratio (SNR) is reduced by 1%, while the sequencing throughput is doubled.

Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing

An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.

Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides

Background

Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths.

Results

To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, cyclic SBL (cSBL), to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction.

Conclusions

Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.