An expanded GGGGCC hexanucleotide (G(4)C(2)) repeat within the non-coding region of C9ORF72 gene has been identified as the most common genetic cause of FTD/ALS kindred, and synthetic ligand targeting this pathological expansion sequence holds a promising approach for the disease interference. We here describe the naphthyridine carbamate tetramer, p-NCTB, as a binding ligand to hairpin G(4)C(2) repeat. p-NCTB simultaneously recognizes two distal CGGG/CGGG sites in G4C2 repeat DNA and RNA leading to the formation of the interhelical (inter-and intrastrand) binding complexes. The intrastrand binding was predominant when p-NCTB bound to long repeat sequence that accommodates multiple binding sites by folding into hairpins, while the interstrand binding was exclusive for short repeat sequence. The binding of p-NCTB showed repeat-length selectivity: the longer repeat sequence is a better target for p-NCTB. p-NCTB demonstrated inhibition of transcription against G(4)C(2) repeat template in vitro in a repeat length-dependent manner. (c) 2020 Elsevier Inc. All rights reserved.