DNA-Directed Base Pair Opening
Abstract
:1. Introduction
2. Results and Discussion
2.1. DNA Crossovers
2.2. Tight Contacts in DNA Higher-Order Structures and Supercoiling
2.3. DNA-Directed Base-Pair Opening
2.3.1. Close Helical Approach and Base Stacking Alterations
Bdjb77 | Bd0015 | Bd0084 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Prop. | Buckle | Dist. | Prop. | Buckle | Dist. | Prop | Buckle | Dist. | |||
(°) | (°) | P-axis | (°) | (°) | P-axis | (°) | (°) | P-axis | |||
(Å) | (Å) | (Å) | |||||||||
C1-G20 | −5.2 | 10.2 | C1-G20 | −8.7 | 6.8 | P(15) | C1-G20 | −11.6 | −0.4 | ||
8.2 | |||||||||||
C2-G19 | 0.6 | 1.4 | C2-G19 | −9.9 | −6.6 | P(14) | C2-G19 | 15.6 | 1.4 | ||
6.6 | |||||||||||
I3-C18 | −10.1 | −0.5 | G3-C18 | −14.5 | −12.2 | G3-C18 | −7.0 | 1.4 | |||
I4-C17 | −6.8 | −2.6 | C4-G17 | −30.6 | 1.8 | P(18) | A4-T17 | 5.7 | −3.3 | ||
8.1 | |||||||||||
I5-C16 | −12.4 | 1.9 | C5-G16 | − 9.2 | 6.5 | P(17) | G5-C16 | −24.5 | −5.4 | P(A14) | |
6.9 | 9.8 | ||||||||||
C6-I15 | −15.2 | −0.7 | P(10) | G6-C15 | −11.4 | −1.8 | C6-G15 | −11.0 | 1.2 | ||
7.5 | |||||||||||
C7-I14 | −15.3 | 11.6 | G7-C14 | −26.1 | 0.3 | T7-A14 | −5.8 | 2.0 | |||
C8-I13 | −13.6 | 16.8 | C8-G13 | −14.0 | −3.5 | C8-G13 | −12 | 2.0 | P(T7) | ||
6.8 | |||||||||||
G9-C12 | −6.1 | 4.8 | P(9) | G9-C12 | −28.7 | 3.3 | G9-C12 | −23.3 | −23.4 | P(C6) | |
8.1 | 8.0 | ||||||||||
G10-C11 | −17.3 | 1.6 | G10-C11 | −16.8 | −4.7 | G10-C11 | −14.9 | 6.3 |
2.3.2. Close Helical Approach and Base Pair Opening
2.3.2.1. Direct Base-Pair Opening
Space group | Resol. | Sequence | Structural alteration | |
---|---|---|---|---|
Base unstacking | ||||
Bdjb77 (286D) | P31 | 2.5 | 5'-CC I I I CCCGG | High propeller twist and buckle values (from C6-I15 to C8 I13) in front of inserted phosphate groups (Table 1) |
3'-GGCCC I I I CC | ||||
Bd0015 (1QC1) | H 3 | 2.5 | 5'-CCGCCGGCGG | Alterations of base stacking along the whole structure (Table 1) |
3'-GGCGGCCGCC | ||||
Bd0084 (1ZFG) | P31 | 1.75 | 5'-CCGAGCTCGG | Alterations of base stacking in front of the inserted phosphate groups (Table 1) |
3'-GGCTCGAGCC | ||||
Direct base-pair opening | ||||
Bd0022 (1QP5) | H 3 | 2.6 | * * | C3-G17(#): N4-O1P: 2.4 Å |
C21-G17(#): N4-O1P: 3.3 Å | ||||
C18-C20(#): N4-O1P: 2.9 Å | ||||
* * | Shift of the base pairing in the major groove (Figure 5) from | |||
Bdl035 (330D) | H 3 | 2.7 | 5'-ACCGCCGGCGCC | Normal base-pairing |
3'-TGGCGGCCGCGG | ||||
Bd0076 (1ZEW) | C2 | 2.25 | C12-G7(#): N4-O1P: 2.7 Å | |
: N4-O6: 4.0 Å | ||||
N3-N1: 3.3 Å | ||||
O2-N2: 2.7 Å | ||||
: O4-N6: 3.6 Å | ||||
* | N3-N1: 3.6 Å | |||
A18-T15(#) N6-O1P: 6.9Å | ||||
: N6-O4 : 4.0 Å | ||||
N1-N3: 3.7 Å | ||||
Bd0028 (1ZFH) | C2 | 2.5 | 5'-CCGCTAGCGG | Normal base-pairing |
3'-GGCGATCGCC | ||||
Bd0021 (1CW9) | P212121 | 1.55 | * | C6-G10(#): N4-O1P: 3 Å |
: N4-O6: 7.0 Å | ||||
3'-GGTCCGGACC | (2 mol/au: open and closed form) | |||
Indirect base-pair opening | ||||
Bdf062 (206D) | P6122 | 2.5 | * | C1-C8(#): N4-O1P: 3.3 Å |
C10-A9(#): C6-O1P: 2.9 Å | ||||
C5-O2P: 3.3 Å | ||||
: O4-N6: 4.7 Å | ||||
O2-N6: 2.9 Å | ||||
Unstacking C1/G2/G3 | ||||
Ud0029 (1P4Z) | P6122 | 2 | * | C7-A6(#): N4-O1P: 3.0 Å |
N4-O6: 3.3 Å | ||||
N6-O4: 3.8 Å | ||||
* | N1-N3: 3.5 Å | |||
Bd0068 (1S1K) | P6122 | 1.9 | 5'-CCMGTACTGG | Normal base-pairing |
3'-GGTCATGMCC | ||||
M=1AP |
2.3.2.2. Indirect Base-Pair Opening
2.4. A Model for the Initiation of DNA Melting Induced by Compaction
3. Conclusions
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Timsit, Y. DNA-Directed Base Pair Opening. Molecules 2012, 17, 11947-11964. https://doi.org/10.3390/molecules171011947
Timsit Y. DNA-Directed Base Pair Opening. Molecules. 2012; 17(10):11947-11964. https://doi.org/10.3390/molecules171011947
Chicago/Turabian StyleTimsit, Youri. 2012. "DNA-Directed Base Pair Opening" Molecules 17, no. 10: 11947-11964. https://doi.org/10.3390/molecules171011947