A cytidinyl derivative, N⁴-(6-aminopyridin-2-yl)-2?-deoxycytidine (^pC), could interact with a CG base pair to support the triple-helix (triplex) formation of oligodeoxyribonucleotides. Characteristics of ^pC in the formation of both intramolecular triplex, i.e., a "paper clip type" triplex (PCT) and intermolecular triplex, i.e., a "linear type" triplex (LT) was monitored by optical methods and isothermal titration calorimetric measurements. Experimental results revealed that the LT with ^pC·CG internally was independent of the solution pH. Only single substitution of ^pC, situated internally but not terminally, facilitated the PCT formation by the UV thermal melting study at the neutral pH. However, the best stabilization of the PCT in acidic conditions occurred when ^pC at the end of the triplex rather than internally. In addition, an LT, but not a PCT, containing an alternating ^pCT^pCT^pC sequence, could be formed in the conditions of 20 mM MgCl₂ and/or 5 mM spermine. Thus, the presence of several nucleotides of ^pC in proximity along the Hoogsteen strand may lead to structural distortion such that the more flexible LT with multiple substitutions is formed in favor of the more rigid PCT.