Table I.

Summary of the DNA-Targeting Small Molecules as Drugs or Therapeutic Candidates

Entry	Name	Chemical structure	DNA sequences	PDB	Ref.
(A) Covalent binders
1	Cisplatin		5′-CCTCTGGTCTCC-3′ 3′-GGAGACCAGAGG-5′	1AIO 3LPV	15, 16
2	Cisplatin		5′-CCUCTCTGGACCTTCC-3′ 3′-GGAGAGACCTGGAAGG-5′	1CKT	18
3	Cisplatin		5′-TCTTCTGTGCTCACCAC-3′ 5′-GTGGTGAGC-3′	2WTF	20
4	Nitrogen mustard		5′-(CGCGAATTCGCG)2-3′	2QEF	25
5	Mitomycin C		5′-ICACGTCIT-3′ 3′-CGTGCAGCA-5′	199D	27
6	2,7-diaminomitosene		5′-(GTGGTATACCAC)2-3′	1JOI	28
7	4′-(hydroxymethyl)-4,5′, 8-trimethylpsoralen		5′-(CCGGTACCGG)2-3′	204D	29
8	AFB-FAPY		5′-CTATGATTCA-3′ 3′-GATACTAAGT-5′	2KH3	33
(B) Minor and major groove binders
9	DAPI		5′-(CGCGAATTCGCG)2-3′	1D30	52
10	Berenil		5′-(CGCGAATTCGCG)2-3′	2DBE	54
11	Pentamidine		5′-(CGCGAATTCGCG)2-3′	1D64	55
12	Hoechst 33258		5′-(CGCGAATTCGCG)2-3′	8BNA	53
13	Netropsin		5′-(C5-BrCCCCIIIII)2-3′	358D	51
14	Distamycin		5′-d(GTATATAC)2-3′	378D	55
15	8-ring cyclic Py-Im polyamide-α		5′-(CCAGGCCTGG)2-3′	315L	66
16	8-ring cyclic Py-Im polyamide-β		5′-(CCAGTACTGG)2-3′	3OMJ	70
17	KWKK		5′-GCTAGCGAGTCC-3′ 3′-CGATCGCTCAGG-5′	2KV6	76
18	Pentamidine		5′-(ATATATATAT)2-3′	3EY0	78
19	Hoechst 33258		5′-(CGCGGATfUCGCG)2-3′	3AJK	80
20	DB921		5′-(CGAATTCGCG)2-3′	2B0K	84
21	DB1055		5′-(CGCGAATTCGCG)2-3′	2I5A	85
22	Netropsin		5′-(CTTAATTCGAATTAAG)2	1ZTT	86
23	CD27		5′-(CTTAATTCGAATTAAG)2	3FSI	87
24	NCSi-gb		5′-CCCGATGC-3′ 3′-GGGCTTAACG-5′	1KVH	98
25	NCSi-glu		5′-(GCCAGAGAGC)2-3′	1MP7	99
26	Neomycin-Hoechst- NH1		5′-(CGCAAATTTGCG)2-3′	Model	103
27	Neomycin-Hoechst- NH2		5′-(CGCAAATTTGCG)2-3′	Model	103
28	Neomycin-Hoechst- pyrene (NHP)		5′-(CGCAAATTTGCG)2-3′	Model	104
(C) Intercalators
29	Daunomycin		5′-(dC)(rG)d(ATCG)2-3′	1D10	124
30	Adriamycin		5′-d(CGATCG)2-3′	1D12	118
31	Ditercalinium		5′-d(CGCG)2-3′	1D32	131
32	Echinomycin		5′-d(GCGTACGC)2-3′	1PFE	140
33	Echinomycin		5′-(ACGTACGT)2-3′	2ADW	141
34	Cryptolepine		5′-(CGTACG)2-3′	1K9G	143
(D) Multimode binders
35	PBD-BIMZ		5′-(AACAATTGTT)2-3′	2KTT	147
36	PDB-naphthalimide		5′-d(AACAATTGTT)2-3′	2KY7	148
(E) Quadruplex binders
37	Daunomycin		5′-d(TGGGGT)4-3′	1O0K	163
38	Distamycin A		5′-d(TGGGGT)4-3′	2JT7	166
(F) Bulge, junctions and phosphate backbone binders
39	SCA-α2		5′-(CCATCGTCTACCTTTGGT AGGATGG)2-3′	2OEY	99
40	DDI		5′-CACGCAGTTCGGAC-3′ 5′-GTCCGATGCGTG-3′	1P96	171
41	ent-DDI		5′-CACGCAGTTCGGAC-3′ 5′-GTCCGATGCGTG-3′	1R4E	172
42	[Rh(bpy)2chrysi]3+		5′-(CGGAAATTCCCG)2-3′	2O1I	173
43	Naphtyridine- azaquinoline (NA)		5′-CTAACAGAATG-3′ 5′-CATTCAGTTAG-3′	1 × 26	174
44	NPM		5′-(CGTACG)2-3′	2ET0	174
45	A4C		5′-(TCGGTACCGA)2-3′	2GWA	182
46	TriplatinNC		5′-(CGCGAATTCGCG-3′)2	2DYW	183