DNA Double Helix Structure
The structural details presented in this tutorial are based on DNA Replication, 2nd edition, by Kornborg and Baker.
Base Pairing
A-DNA
<> Load a model of A-DNA. The A-DNA duplex structure is also typical of RNA duplexes because the ribose 2'-hydroxyl clashes with the phosphate group of the adjacent nucleotide, preventing the formation of the B-form duplex. Compared to B-form DNA, the A-DNA structure is more uniform, has a deeper but narrower major groove, and a repeat distance of 11 to 12 base pairs. These features result from C3'-endo sugar pucker (instead of C2'-endo pucker found in B-form DNA) and base pair slide. C3'-endo Sugar Pucker <> A major difference between A and B DNA structure is caused by different sugar puckers. In A-DNA, the ring of the ribose has the C3'-endo configuration, with the carbon 3 (yellow spacefilled atom) raised above the plane of the sugar ring, while carbon 2 (red spacefilled atom) is below the plane. In B-DNA, the ring is in the C2'-endo configuration, with the C2 atom above the sugar plane and the C3 atom below it. The altered sugar puckering shortens the distance between adjacent phosphates by about 1 angstrom, giving 11 to 12 base pairs per helix in A-DNA, instead of 10.5 in B-DNA. Can you imagine how changing the sugar pucker would bring the 3'-phosphate closer to the 5'-phosphate? Base-pair Slide In B-DNA, the base pairs are centered over the helix axis. In A-DNA, the base pairs slide ~5 Angstroms away from the helix center <> Reload the A-DNA duplex, and highlight a dinucleotide step to illustrate the slide. <> Zoom in on the dinucleotide step. Notice how the brown colored base pair is slid to the left relative to the cyan colored base pair. Note that the slide and sugar pucker give: <> a uniform, ribbon shaped helix <> a cylindrical open core <> a very deep major groove that is more narrow than the one found in B-DNA B-DNA <> B-DNA has a more varied structural topology than A-DNA. <> This results from the C2'-endo pucker, and <> central stacking of the base pairs Relative to A-DNA, its features are <> 10.5 base pairs per helical turn count the base pairs per turn also note the central stacking of basepairs <> a narrowed minor groove, relatively devoid of functional groups for making specific contacts with proteins re-run the script to watch the major and minor grooves move right to left as the molecule rotates <> highlight the atoms of the minor groove (red) and a widened major groove with a diverse set of functional groups that can be used to form specific contacts with DNA binding proteins <> highlight the atoms of the major groove (cyan) <> show both minor and major groove atoms together <> show both minor and major groove atoms together, identifying atoms by cpk color, with backbone in yellow Major Groove Minor Groove Adenine C6, N6, C5, N7, C5 C2, N3, C4, N9 Guanine C6, O6, C5, N7, C8 C2, N2, N3, C4, N9 Cytosine C6, C5, C4, N4 O2, N1, C2 Thymine C6, C5, C4, O4, C5M O2, C2, N1, C6 Z-DNA Z-DNA was discovered in crystals of d(CGCGCG). It has <> a left handed helix (right handed in A-DNA and B-DNA) <> a dinucleotide repeat structure, with alternating anti and syn orientations of the glycosyl bonds (all anti in A-DNA and B-DNA) C2'-endo and C3'-endo sugar puckers (C2'-endo in B-DNA, C3'-endo in A-DNA) Use the following table to help you identify the parts: Nucleotide 1 Nucleotide 2 Phosphate red orange 2-deoxy-ribose cyan C2'-endo in spacefill blue C3'-endo in spacefill Base green, in anti orientation white, in syn orientation The model is centered on C2' of nucleotide 1. anti - base rotated out, away from the ribose plane syn - base rotated in, over the ribose plane <> twist angles of 15° (CpG step) and 45° (GpC step) the first CpG (red/yellow) base pair has a small twist, but the twist between the 2nd and 3rd base pairs (GpC - yellow/cyan) is large as the dinucleotide repeat unit begins again (CpG), so does the small twist (cyan/green) DNA Bending Long chains of duplex DNA are very flexible, but ones less than ~100 bp are not. The lateral backbones resist sliding because the ribose ring and phosphates have little freedom to move. Twisting is restricted by requiring over- or under-winding of the DNA duplex. Nonetheless, the fairly rigid rod can be bent. Such bends are intrinsic to a given sequence, or result from the actions of DNA binding proteins. Examples Intrinsic sequences <> Runs of A-tracts Here, the action of a drug called bizelesin (green) illustrates the ability of A-tract DNA (A's cyan, T's yellow) to bend by widening the minor groove and narrowing the major groove. Such bending also occurs in the absence of the drug. When A-tracts are repeated, the intrinsic bends of each section add or cancel depending on their phasing. Several repeats of phased A-tracts can create very large bends. glnA promoter region In this system An activation sequence binds an activator (NtrC) The activator contacts RNA polymerase at the promoter via a DNA-looping mechanism Upon ATP hydrolysis by the activator, the promoter region opens to permit transcription. <> The wild type sequence predicts additive curvature centered at -77, between the activator binding site (red) and promoter (blue) The predicted trajectories for two promoter regions are superimposed wild type glnA (biggest bend) glnA* bearing a point mutation at -77 that reduces predicted curvature and bending, and reduces promoter strength Note: depending on which programs one uses, the predicted bendability and curvature vary significantly, reflecting our incomplete understanding of factors that influence bending genetic systems similar to gln use IHF-binding at -33 to -77 to facilitate the looping mechanism (see below for IHF DNA bending) Protein Induced Bends <> Cap - cyan and blue for protein, cpk colors for DNA <> IHF - blue and cyan for protein subunits, yellow and orange for DNA <> TBP - red for TBP protein, black and yellow for DNA
Compared to B-form DNA, the A-DNA structure is
These features result from C3'-endo sugar pucker (instead of C2'-endo pucker found in B-form DNA) and base pair slide.
B-DNA
<> B-DNA has a more varied structural topology than A-DNA. <> This results from the C2'-endo pucker, and <> central stacking of the base pairs Relative to A-DNA, its features are <> 10.5 base pairs per helical turn count the base pairs per turn also note the central stacking of basepairs <> a narrowed minor groove, relatively devoid of functional groups for making specific contacts with proteins re-run the script to watch the major and minor grooves move right to left as the molecule rotates <> highlight the atoms of the minor groove (red) and a widened major groove with a diverse set of functional groups that can be used to form specific contacts with DNA binding proteins <> highlight the atoms of the major groove (cyan) <> show both minor and major groove atoms together <> show both minor and major groove atoms together, identifying atoms by cpk color, with backbone in yellow Major Groove Minor Groove Adenine C6, N6, C5, N7, C5 C2, N3, C4, N9 Guanine C6, O6, C5, N7, C8 C2, N2, N3, C4, N9 Cytosine C6, C5, C4, N4 O2, N1, C2 Thymine C6, C5, C4, O4, C5M O2, C2, N1, C6 Z-DNA Z-DNA was discovered in crystals of d(CGCGCG). It has <> a left handed helix (right handed in A-DNA and B-DNA) <> a dinucleotide repeat structure, with alternating anti and syn orientations of the glycosyl bonds (all anti in A-DNA and B-DNA) C2'-endo and C3'-endo sugar puckers (C2'-endo in B-DNA, C3'-endo in A-DNA) Use the following table to help you identify the parts: Nucleotide 1 Nucleotide 2 Phosphate red orange 2-deoxy-ribose cyan C2'-endo in spacefill blue C3'-endo in spacefill Base green, in anti orientation white, in syn orientation The model is centered on C2' of nucleotide 1. anti - base rotated out, away from the ribose plane syn - base rotated in, over the ribose plane <> twist angles of 15° (CpG step) and 45° (GpC step) the first CpG (red/yellow) base pair has a small twist, but the twist between the 2nd and 3rd base pairs (GpC - yellow/cyan) is large as the dinucleotide repeat unit begins again (CpG), so does the small twist (cyan/green) DNA Bending Long chains of duplex DNA are very flexible, but ones less than ~100 bp are not. The lateral backbones resist sliding because the ribose ring and phosphates have little freedom to move. Twisting is restricted by requiring over- or under-winding of the DNA duplex. Nonetheless, the fairly rigid rod can be bent. Such bends are intrinsic to a given sequence, or result from the actions of DNA binding proteins. Examples Intrinsic sequences <> Runs of A-tracts Here, the action of a drug called bizelesin (green) illustrates the ability of A-tract DNA (A's cyan, T's yellow) to bend by widening the minor groove and narrowing the major groove. Such bending also occurs in the absence of the drug. When A-tracts are repeated, the intrinsic bends of each section add or cancel depending on their phasing. Several repeats of phased A-tracts can create very large bends. glnA promoter region In this system An activation sequence binds an activator (NtrC) The activator contacts RNA polymerase at the promoter via a DNA-looping mechanism Upon ATP hydrolysis by the activator, the promoter region opens to permit transcription. <> The wild type sequence predicts additive curvature centered at -77, between the activator binding site (red) and promoter (blue) The predicted trajectories for two promoter regions are superimposed wild type glnA (biggest bend) glnA* bearing a point mutation at -77 that reduces predicted curvature and bending, and reduces promoter strength Note: depending on which programs one uses, the predicted bendability and curvature vary significantly, reflecting our incomplete understanding of factors that influence bending genetic systems similar to gln use IHF-binding at -33 to -77 to facilitate the looping mechanism (see below for IHF DNA bending) Protein Induced Bends <> Cap - cyan and blue for protein, cpk colors for DNA <> IHF - blue and cyan for protein subunits, yellow and orange for DNA <> TBP - red for TBP protein, black and yellow for DNA
Relative to A-DNA, its features are
Z-DNA
Z-DNA was discovered in crystals of d(CGCGCG).
It has
Use the following table to help you identify the parts:
DNA Bending