Table 1.

Summary of existing methodologies for identification of Z-DNA

Category	Subtype	Methodology	Refs
Biophysical methods	Spectroscopy	CD	[1,3–5]
		IR spectroscopy	[6]
		Raman spectroscopy (including surface-enhanced Raman)	[7,8]
	NMR	Solution-state NMR	[7,9,10]
	X-ray diffraction	Single-crystal X-ray diffraction	[2,11]
	Fluorescence techniques	FRET (Z-to-B transition monitoring)	[12]
		smFRET	[13]
	Hydrogen exchange kinetics	HDX	[14]
	Thermodynamic analysis	ITC	[15]
		DSC	[15]
Biochemical methods	Electrophoresis	Native/denaturing gel electrophoresis	[16–20]
	Torque spectroscopy	Single-molecule torque measurements	[21,22]
	Ultracentrifugation	Sedimentation analysis	[23]
	Membrane-binding assays	Nitrocellulose filtration	[24]
	Ligand-based detection	Ruthenium complex groove binding	[24]
	Nuclease sensitivity	DNase I/restriction enzyme cleavage assays	[25,26]
	Chemical probes	Bromine/OsO4/DEPC modification	[27,28]
Antibody/protein based	High-throughput profiling	ZαADAR1 ChAP-seq	[34]
		Zaa-FLAG ChIP-seq	[30]
		Z22 antibody-based ZIP-seq/ChIP-seq/CUT&TAG	[35,36]
Computational prediction	Algorithmic tools	Z-Hunter	[32]
		DeepZ (machine learning)	[29,32]
		Z-DNABERT/ZSeeker	[33]
		nBMST	[29]
Protein-independent methods	Genome-wide mapping	ssDNA mapping + PZFS overlap	[37]
		ViCAR Hi-C adaptation	[38,39]