What does sequence-dependent mean?

Question

[dadiwi8427]

What does it mean for a DNA bend to be sequence dependent?

Answer 1

[Mensur Dlakic]

Like all long polymers, DNA is subject to thermal motions that cause it to adopt various shapes. Persistence length of is the length at which a molecule is expected to behave more or less as a straight rod. DNA is among the stiffest polymers, and persistence length of random DNA molecules is 35-50 nm (100-150 base pairs). This is to say that there are thermal motions that will cause small local bends in a molecule, but they usually don't amount to much for short DNA molecules. In practical terms, it is very difficult to cyclize DNA molecules shorter than 200 base pairs.

Sequence-depending bending refers to the ability of certain DNA sequences to create stable curvature that shortens persistence length of DNA. For example, multiple stretches of 4-5 adenines, especially when separated by a multiple of helical turns (10.5 bp on average), cause curvature in DNA. The same is true for repeated GGGCCC sequences. Local bending parameters can be derived for each individual DNA dinucleotide, but in most cases it is a cumulative effect of certain sequences that causes curvature (which is a synonym with global bending).

Largest DNA bends are caused by dedicated DNA-bending proteins, which can literally create a U-turn (a 180-degree bend) over 20 or so base pairs. Those are referred to as DNA kinks, because there are usually a couple of large structural distortions caused by protein side-chains (usually aromatic) wedging themselves between DNA bases. They cause kinks that are rarely seen in free DNA molecules. See TATA-binding protein (TBP) and integration host factor (IHF) for examples of protein-induced DNA kinking, and catabolite repressor protein (CRP) for protein-induced DNA bending.

Answer 2

[seidel]

It means that the DNA exhibits a bent state, and the bend is dependent on the sequence of the DNA. If the sequence is changed, the bend will not occur.