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Open Access Methodology article

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

Antoine Ho1, Maurice Murphy23, Susan Wilson23, Susan R Atlas234 and Jeremy S Edwards125*

Author affiliations

1 Department of Molecular Genetics and Microbiology, University of New Mexico. Albuquerque, New Mexico, USA

2 Cancer Center, University of New Mexico. Albuquerque, New Mexico, USA

3 Center for Advanced Research Computing, University of New Mexico. Albuquerque, New Mexico, USA

4 Department of Physics and Astronomy, University of New Mexico. Albuquerque, New Mexico, USA

5 Department of Chemical and Nuclear Engineering, University of New Mexico. Albuquerque, New Mexico, USA

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Citation and License

BMC Genomics 2011, 12:598  doi:10.1186/1471-2164-12-598

Published: 12 December 2011

Abstract

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.