User:Karsten Theis/DNA bulges

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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].

Bulges in 3D

The NMR structure [2] of a 5 nucleotide bulge shows a sharp bend (kink) in the DNA, with all nucleotides stacked. On the other hand, the X-ray structure of a 1-nucleotide bulge 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.[3].

More examples:

  • Ligase bound to bulged DNA pre-ligation 7kr3
  • 5-nt bulge, AATAA 1jrv
  • 2-nt bulge with bound molecule 1p96
  • 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


NMR structure 1js5 of a DNA duplex with a AAUAA insertion in one strand, causing a bulge.
Drag the structure with the mouse to rotate

Modelling bulges

Using a course-grained model, Schreck et al [4] concluded that there are several possibilities to accommodate a bulge:

"

  • A: The bases in the loop disrupt the duplex as little as possible and are flipped out, which results in almost no bending.
  • B: The bases from the bulge loop are inserted into helix while maintaining stacking opposite the bulge, resulting in some degree of static bending away from the bulge.
  • C: A combination of A and B in which some bases are inserted into the helix, while others are flipped out.
  • D: The stacks opposite and across from the bulge are broken, resulting in increased flexibility and a large static bend

"

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ doi: https://dx.doi.org/10.1063/1.4917199

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Karsten Theis

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