HnRNP-A1 binds directly to double-stranded DNA in vitro within a 36 bp sequence

The heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) is known as an RNA- and single-stranded DNA-binding protein involved in alternative splicing of mRNA, RNA transport and maintenance of chromosome telomere length. In this study we tested whether this protein could bind directly to double-stranded DNA (dsDNA). Using PCR amplification of target DNA-sequences from human chromosome 11q13 followed by their incubation with hnRNP-A1 and atomic force microscopy (AFM) of the DNA/protein complexes, we found that this protein bound to DNA within a 36 bp sequence. These results were confirmed by electrophoretic mobility shift assay (EMSA). This sequence was found widely dispersed throughout the genome. There is no overlap between the 36 bp sequence and known target sequences in RNA for binding hnRNP-A1.