Table 1.
Average backbone-base pair inclinations ηB in non-standard nucleic acid structures, involving parallel (ps) and antiparallel (aps) orientation of strands and various base pairing modes1
| Sequence and synopsis | NDB code | Reference | Base pair | Pairing mode | Strand polarity | ηB (σ) Strand 1 | ηB (σ) Strand 2 |
|---|---|---|---|---|---|---|---|
| d(CCCC) self-intercalated i-motif paired via C C+ base pairs | UDD024 | (13) | C1–C5 to C4–C8 | rWC | ps | +0.9° (4.1°) | +1.8° (2.0°) |
| C9–C13 to C12–C16 | rWC | ps | +2.7° (0.1°) | +0.6° (2.5°) | |||
| d(CGATCG) ps duplex at low pH with homo base pairing | supporting information (NMR solution structure) | (10) | G2–G8 to C5–C11 (PSte model2) | rWC | ps | −1.5° (12.8°) | −1.5° (12.8°) |
| G2–G8 to C5–C11 (PSts model2) | rWC | ps | −0.4° (13.1°) | −0.4° (13.1°) | |||
| d(CGCGCG)3 left-handed Z-DNA duplex | ZDF035 | (45) | G2–C11 to C5–G8 | WC | aps | +20.8° (8.9°) | +20.5° (10.3°) |
| d(ATATAT) duplex with Hoogsteen pairs only | UD0035 | (46) | T2–A11 to A5–T8 | Hoogsteen | aps | −7.3° (6.0°) | −6.0° (5.1°) |
| r(GACACCUGAUUC)/ d(GAATCAGGTGTC) RNA–DNA hybrid bound to RNase H | PH0016 | (47) | rA2–dT11 to rU10–dA3 | WC | aps | −25.2° (5.6°) | −33.2° (9.0°) |
| dd(CGAATTCG) homo-DNA duplex | UD0070 | (28) | G2–C15 to C7–G10 | WC | aps | +34.3° (10.9°) | +35.5° (10.8°) |
| pr(CGAATTCG) pyranosyl- RNA duplex | – (NMR solution structure) | (26) | G2–C15 to C7–G10 | WC | aps | −46.2° (3.8°) | −46.2° (4.2°) |
| d(TGGGGT) parallel-stranded tetraplex with four G-quartets | UDF036 | (48) | G2–G12 to G5–G15 | Hoogsteen (adjacent strands) | ps | +19.4° (11.7°) | −20.6° (3.0°) |
| G2–G32 to G5–G35 | Hoogsteen (diagonally related strands) | ps | −31.6° (9.5°) | +26.1° (11.6°) | |||
| d(GGGGBrUTTTGGGG) antiparallel-stranded tetraplex with four G-quartets | UD0013 | (49) | G1001–G2009 to G1004–G2012 | Hoogsteen (adjacent strands) | aps | +17.0° (8.1°) | +29.7° (7.2°) |
| G1001–G1012 to G1004–G1009 | Hoogsteen (diagonally related strands) | aps | +0.5° (8.4°) | +2.2° (7.4°) | |||
| p(CGTACG)4 peptide nucleic acid duplex | UPNA56 | (50) | G2–C12 to C5–G9 | WC | aps | −35.5° (1.6°) | −32.8° (1.5°) |
| d(TCCTCCTTTTTTAGGA GGATTTTTTGGTGGT) intramol. Pu-Pu–Py type triplex with G–G–C and T–A–T triples (T loops underlnd.) | Protein Data Bank entry 134D | (52) | C2–G13 to C6–G9 | WC | aps | −25.5° (8.9°) | −22.6° (4.4°) |
| (NMR solution structure) | G9–G20 to G13–G16 | Hoogsteen and reverse Hoogsteen | aps (Pu) ps (Py) | +10.6° (12.5°) | +24.1° (9.3°) |
1Using a Bspline curve for the phosphate backbone.
2Parallel Stranded extended model [PSte; rWC like, symmetrical type I (A), type III (G) homo-purine and type XII (T), type XIV (C) homo-pyrimidine pairing] and Parallel Stranded short model [PSts; symmetrical type II (A), type IV (G) homo-purine and type XIII (T), type XV (C) homo-pyrimidine pairing] (30).
3Defining the backbone by P → P vectors may be superior to the BSpline approach due to the zigzag shape of the Z-backbone.
4Right-handed conformation of the PNA duplex; BSpline curve through C5′ atoms.