Direct detection of alpha satellite DNA with single-base resolution by using abasic Peptide Nucleic Acids and Fluorescent in situ Hybridization

The detection of repetitive sequences with single-base resolution is becoming increasingly important aiming to understand the biological implications of genomic variation in these sequences. However, there is a lack of techniques to experimentally validate sequencing data from repetitive sequences obtained by Next-Generation Sequencing methods, especially in the case of Single-Nucleotide Variations (SNVs). That is one of the reasons why repetitive sequences have been poorly studied and excluded from most genomic studies. Therefore, in addition to sequencing data, there is an urgent need for efficient validation methods of genomic variation in these sequences. Herein we report the development of chemFISH, an alternative method for the detection of SNVs in repetitive sequences. ChemFISH is an innovative method based on dynamic chemistry labelling and abasic Peptide Nucleic Acid (PNA) probes to detect in situ the α-satellite DNA, organized in tandem repeats, with single-base resolution in a direct and rapid reaction. With this approach, we detected by microscopy the α-satellite DNA in a variety of human cell lines, we quantified the detection showing a low coefficient of variation among samples (13.16%–25.33%) and we detected single-base specificity with high sensitivity (82.41%–88.82%). These results indicate that chemFISH can serve as a rapid method to validate previously detected SNVs in sequencing data, as well as to find novel SNVs in repetitive sequences. Furthermore, the versatile chemistry behind chemFISH can lead to develop novel molecular assays for the in situ detection of nucleic acids. [Display omitted] •ChemFISH for the detection of α-satellite DNA with single-base resolution in a rapid and direct reaction.•Detection of α-satellite DNA in different human cell lines with low variability (Coefficients of Variation 13.16%-25.33%).•High sensitivity detecting single-base specificity (from 82.41% to 88.82%).•ChemFISH can be used as a tool to detect novel Single-Nucleotide Variations (SNVs) in repetitive sequences such as the human α-satellite DNA.•The method will contribute to the development of novel molecular assays for nucleic acids imaging by fluorescent microscopy.