Background/Aim. Long non-coding RNAs (lncRNAs) are candidate regulators of cardiac stress responses, yet their sequence-level mechanisms remain undercharacterised. Extending our prior computational analysis of rat cardiac hypoxia [1], we systematically characterised triplex-forming and G-quadruplex-forming lncRNA candidates across four independent rat cardiovascular stress models. Methods. 52 differentially expressed lncRNAs (padj < 0.05, |log2FC| ≥ 1—2; DESeq2) from four GEO RNA-seq datasets — GSE245300 (hypobaric hypoxia [2]), GSE284606 (ischaemic preconditioning [3]), GSE186989 (SU5416/hypoxia PAH + chrysin [4]) and GSE317340 (donation after circulatory death, male/female/OVX [5]) — were analysed using canonical spliced transcript sequences (mRatBN7.2/Ensembl 108), rgt-TDF v1.0.2 (promotertest; −l 15 −e 20), RNAfold 2.4.7, and G4Hunter ∩ QGRS quadruplex detection. Results. 29 of 52 lncRNA candidates showed significant triplex-forming potential (p < 0.05); three appeared in two or more independent datasets, including Nupr1l1 — upregulated in both PAH right ventricle and donation-after-circulatory- death left ventricle. Seven candidates combined triplex activity with consensus G-quadruplex domains, suggesting dual regulatory capacity. Exploratory comparison of Su/Hx and Su/Hx + chrysin right ventricular transcriptomes revealed no statistically significant differential lncRNA expression after multiple-testing correction (n = 4; limited power); however, 32 lncRNAs showed nominal expression changes (p < 0.05), including candidates dysregulated in Su/Hx vs Control, suggesting preliminary evidence of lncRNA profile responsiveness to pharmacological modulation of the pathological state. Conclusions. RNA-DNA triplex formation is a convergent lncRNA regulatory mechanism across diverse forms of cardiac hypoxia. Cross-dataset candidates with dual triplex/G4 activity — particularly Nupr1l1 — represent priority targets for functional validation. lncRNA profiles show preliminary responsiveness to pharmacological modulation, warranting larger-cohort studies.