User:Karsten Theis/DNA bulges
From Proteopedia
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<StructureSection load='' size='340' side='right' caption='' scene='10/1073371/Bulge5/1'> | <StructureSection load='' size='340' side='right' caption='' scene='10/1073371/Bulge5/1'> | ||
==Bulges in 3D== | ==Bulges in 3D== | ||
| - | The NMR structure <ref>PMID:12060684</ref> of a 5 nucleotide bulge shows a sharp bend (kink) in the DNA, with all nucleotides <scene name='10/1073371/Bulge5/2'>stacked</scene>. On the other hand, the X-ray structure of a <scene name='10/1073371/Bulge1/1'>1-nucleotide bulge</scene> shows looping out of the extra nucleotide in one case, and disruption of stacking in the other strand in the other case. In the crystal structure, however, the looped out nucleotide inserts into the gap in a neighboring molecule, resulting in perfect stacking with an A:A mismatch.<ref>PMID:1593627</ref>. | + | The NMR structure <ref>PMID:12060684</ref> of a 5 nucleotide bulge shows a sharp bend (kink) in the DNA, with all nucleotides <scene name='10/1073371/Bulge5/2'>stacked</scene>. On the other hand, the X-ray structure of a <scene name='10/1073371/Bulge1/1'>1-nucleotide bulge</scene> shows looping out of the extra nucleotide in one case, and disruption of stacking in the other strand in the other case. In the crystal structure, however, the looped out nucleotide inserts into the gap in a neighboring molecule, resulting in perfect stacking with an A:A mismatch.<ref>PMID:1593627</ref>. |
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| + | More examples: | ||
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| + | * Ligase bound to bulged DNA pre-ligation [[7KR3]] | ||
| + | * 5-nt bulge, AATAA [[1JRV]] | ||
| + | * 2-nt bulge with bound moleule [[P96]] | ||
| + | * 2-nt bulge bound to HMG protein [[8R1X]] | ||
| + | * 1-nt bulge bound to argonaute [[5XOW]] | ||
| + | * hairpin Dna_(5'-d(*gp*cp*cp*gp*cp*ap*gp*tp*gp*c)-3') [[2lo8]] | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 19:23, 25 February 2025
DNA bulges are features in double stranded DNA that occur when there is an insertion in one strand but not the other. The inserted nucleotides are unable to pair with the other strand, leading to distortions from canonical B-form duplex DNA. These distortion may involve bends in the DNA, looped out nucleotides or a combination of the two.
Evidence for structural distortions
The classic evidence is a mobility shift assay, with bent DNA running slower than straight DNA of the same size (or DNA having the bend in the center vs near the end of a sequence). More recently, FRET has also been used as a way to monitor bending (via a decrease in the distance of the flanking duplex sequences). The bending angle and a twisting angle can be used to characterize the overall effect of the DNA bulge. The structural details at the bulge may be probed by footprinting-type experiments[1].
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References
- ↑ Lilley DM. Kinking of DNA and RNA by base bulges. Proc Natl Acad Sci U S A. 1995 Aug 1;92(16):7140-2. PMID:7543675 doi:10.1073/pnas.92.16.7140
- ↑ Gollmick FA, Lorenz M, Dornberger U, von Langen J, Diekmann S, Fritzsche H. Solution structure of dAATAA and dAAUAA DNA bulges. Nucleic Acids Res. 2002 Jun 15;30(12):2669-77. PMID:12060684
- ↑ Joshua-Tor L, Frolow F, Appella E, Hope H, Rabinovich D, Sussman JL. Three-dimensional structures of bulge-containing DNA fragments. J Mol Biol. 1992 May 20;225(2):397-431. PMID:1593627
