DNA Grooves. B DNA double helix displays a nm pitch including a wider (major) and a narrower (minor) groove (furrow) along its helical structure. Molecules The major groove is 12 Angstroms wide, while the minor groove is 6 Angstroms wide. The major groove is slightly deeper than the minor groove ( versus Angstroms). The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together. The grooves twist around the molecule on opposite sides. Certain proteins bind to DNA to alter its structure or to regulate transcription (copying DNA to RNA) or replication (copying DNA to DNA) A-DNA has minor and major grooves of almost equal size, and in Z-DNA, major groove does not exist while minor groove is deep and narrow (Ussery ). We describe the synthesis of new environmentally sensitive fluorescence probes to elucidate DNA structures. DNA oligonucleotides containing fluorophore dan (6-(dimethylamino)acylnaphthalene)-modified dC or dG were able to monitor the microenvironmental changes in both the major and minor grooves of DNA with a B- to To aim for a comprehensive review to cover all aspects related to DNA targeting would be an impossible task and, hence, the objective of the present review is High resolution three-dimensional structures for five different architectural proteins complexed to their cognate DNA sites have been solved to date and include (a) TATA Each groove is lined by potential hydrogen-bond donor and acceptor atoms of the bases that enable specific interactions with proteins. The larger size of the major groove
Discovery of the structure of DNA (article) | Khan Academy
The DNA-binding domain of Tn transposase uses a β-sheet to bind the major groove and a loop to engage the minor groove. However, the minor groove contacts of the Tn DNA-binding domain are predominantly with the phosphate backbone rather than with the bases, and therefore do not appear to be sequence-specific Existing structural evidence suggests that there is little, if any, change in the conformation of DNA or the minor groove binder on association. Therefore, the minor groove binding has been considered to be a rigid-body association accompanied by zero conformational free energy change (2,3,9–11). On the other hand, it is always possible DNA major vs minor groove- differences: A DNA major groove is large in size and thus is wider and deeper than the minor groove. Minor groove is smaller in Widths were measured as the distances between opposite phosphates of major and minor grooves. The major and minor groove widths of ideal B-form DNA are shown as two constant values, 17 and 12 Å Several crystallographic, solution-state and theoretical studies carried out this past year provide new support for the sequence-specific nature of monovalent and divalent cation coordination within the DNA major and minor grooves. Correlations observed between groove width and cation coordination i Why do the major and minor groove exist in DNA? (1 answer) Closed 6 years ago. I understand that they arise due to the pairing of bases of two opposite This dissertation describes work focused on the application of polyamide. conjugates, as well as efforts to expand the repertoire of predetermined DNA. sequences amenable to recognition of by minor groove-binding polyamides. Chapter 2 discusses the design and synthesis of fluorophore-polyamide conjugates The major and minor groove width of DNA is almost constant for all the system throughout the simulation (Figs. 3 b and c), however, the average value of the minor and major groove width of DNA in GdmCl is marginally less than the case of urea and water. The data on the groove width indicate the possibility of different interaction of
Strong minor groove base conservation in sequence logos implies DNA …
An increasing number of high-resolution structures suggest that both the minor and major grooves of DNA can function as receptors for proteins and small molecules. In this review, we try to illustrate the diversity of small molecule ligands that are capable of specifically recognizing the minor groove of DNA. Complex formation results in The major groove has multiple sites of interaction, thus offering comparatively strong binding to drugs/ligands [7], [9]. It has a width of Å and depth of [10]. The major groove provides easy access for bulky molecules [11]. On the other hand, the minor groove has less binding sites and is smaller in size, with a depth of Proteins that recognize DNA sequences often do so by interacting with particular combinations of base pairs in major grooves based on these exposed atoms. In the Achieving a partial fit of both HTH motifs into the major groove. (Right) Addition of the F1 roll parameters to the DNA in the middle panel, generating a close fit (RMSD = A