Grooves

Single helical chain to form the DNA backbone. Double helix of another, may be found trace between the strands, the groove or space,. It is close to the base pairs, these cavities may be provided binding sites. In contrast, the element has not been disposed relative to one another, is sized unequal channel. The two channels, on the other hand, the main groove is wide 12 is the width to 22 minor groove. Narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, as may be coupled to specific sequences of double-stranded DNA, usually proteins, such as transcription factors, have contacted the walls of the base defining the main groove. This situation is different in an abnormal conformation of the DNA cell (see below), but a channel large in order to reflect the difference in the amount seen when it is twisted back to form B normal DNA.

Illustration of major and minor DNA grooves

Than others, the interval backbone are close to each other on one side of the filament. can occur when the backbone is far the main channel when they are close to each other, the minor groove is present. I twist the grooves on both sides of the molecule. You can change the structure of them, some proteins bind to DNA in order to for (copy DNA and DNA) or duplicate (copy RNA, the DNA) regulation of transcription. Be interaction for the backbone, DNA-binding proteins of these are not the (inner parts of the DNA molecule) of ground groove larger piece of the way is easy.

DNA smooth side, such as the cylinder regular explore the optical label “phosphate group position”. Please note groove on the surface of the DNA molecule between the phosphate group. In many cases, proteins that interact with DNA comes into contact with these channels. How would you describe the channel surface of the DNA?

Proteins that interact with DNA frequently in contact with the edges of the base pairs to enter the main groove. Available for a group on the edge of the chemical GC base pairs, of the reaction of the secondary channel (right image) basic (left), color-coded pairs of illustrations for each type of interaction in it will be displayed. For more information about the recognition element, the view “. Recognition groove Vice” is located in the “recogniton big bend” on the secondary channel and main

The ° C, energy profile of a significant number of protein-DNA system in the 20 features by unfavorable enthalpy that in spite of the Gibbs free energy equivalent, groove large is compensated by the contribution of good entropy together It was shown to be enthalpy driven process, mainly associated with the minor groove arrive. Power signatures these different for coupling groove little larger pair is independent of the degree of bending of the protein refolding induced by the binding and / or DNA. That the water in the minor groove in the rich T-shirt is located at an altitude, it has been ranked the removal of the contribution of significant positive joint entropy, ie, the main factors of energy different profiles they, different dent of large and small I seem to hydration characteristics. Entropy, since the driving caused by displacement of the water is disposed force minor groove protein, the normal mode of polar contacts, they can not be considered hydrophobic.

Double helix is ​​a molecule of viscosity and stiffness of very small diameter and great distance. This is a minor groove and great groove. Main channel is deep, wide minor groove is shallow and narrow. DNA-protein interactions are the major process / essential in the life of the cell. Non-specific binding boundaries and hydrogen: van der Waals interactions, electrostatic interactions protein binds to the floor channels of the DNA using a specific binding in general. Exclusively the second half of the main groove and recognizes hydrogen bond donnors, H-bond acceptor, metyl group (hydrophobic), there is a possible four models for the recognition of the main groove there, protein 2 only in minor groove.

In the minor groove in the other, to bind DNA in the large channel, some proteins, connects to both easy part. When you have to do something DNA are looking for a “start sequence”, this is a very useful enzyme. In the major groove, you will be able to recognize the base pairs with no development of the double helix always. Incidentally, it is encoded in the order of H H-bond donors are different for each combination group CH3, base pair, a hydrogen bond acceptor. Turn – – helix protein, such as band structure, such as a zinc finger or helix, is attached to the track (-. You, it is necessary to know the order of one of the 5′-> 3 ‘obviously) channel It is useful to recognize the DNA of many.