Base pairs, representation

Figure 35-2. A diagrammatic representation of the Watson and Crick modei of the doubie-heiicai structure of the B form of DNA.The horizontai arrow indicates the width of the doubie heiix (20 A), and the verticai arrow indicates the distance spanned by one compiete turn of the doubie heiix (34 A). One turn of B-DNA in-ciudes ten base pairs (bp), so the rise is 3.4 A per bp. The centrai axis of the doubie heiix is indicated by the verticai rod. The short arrows designate the poiarity of the antiparaiiei strands. The major and minor grooves are depicted. (A,adenine C, cytosine G, guanine ...

Figure 35-7. Diagrammatic representation of the secondary structure of a single-stranded RNA molecule in which a stem loop, or "hairpin," has been formed and is dependent upon the intramolecular base pairing. Note that A forms hydrogen bonds with U in RNA.

Fig. 12 (A) The d(CGCGAATTCGCG)2 duplex with a narrow groove and a sodium ion coordinated at the ApT step. (I) The DNA is shown in stick representation and the ion in space-filling size. Left view is directly into the central minor groove. Right view left view rotated 90° counterclockwise and tilted 30° to show the ion in the minor groove. (II) The base pair views are of the central ApT step. Top view is down the helix axis, bottom view is directly into the minor groove. (B) The DNA duplex with a phosphate-oxygen pair-sodium ion interaction and a water molecule coordinated at the ApT step. (II) Views as in Fig. 12A for the phosphate-ion-water-base complex at the AT site. Reproduced with permission from Ref. (42). Copyright 2000, American Chemical Society.

Fig. 5 Schematic representation of long distance radical cation migration in DNA. In AQ-DNA(3), irradiation of the anthraquinone group linked at the 5 -terminus leads to reaction at GG steps that are 10, 28, 46 and 55 base pairs from the charge injection site. The solid arrows indicate approximately the amount of reaction observed at each GG step. The plot shows the natural log of the normalized amount of reaction as a function of distance from the AQ. The results appear to give a linear distance dependence...

Fig. 10 Two schematic representations of a polaron-like species in DNA. In the top drawing, the base pairs of DNA are represented by the horizontal lines the sugar diphosphate backbone is represented by the vertical lines. The polaronic distortion is enclosed in the box and extends over some number of base pairs. This is shown schematically by drawing the base-pair lines closer together. In the lower figure, a specific potential po-laron is identified, AAGGAA, and the radical cation is presented as being delocalized over this sequence. Movement of the polaron from one AAGGAA sequence to the next requires thermal activation...

Fig, 11. Diagrammatic representation of a planar intercalating guest molecule complexed between adjacent base pairs of the double helical DNA host structure. The base pairs and intercalator are represented by stippled rods. Note the increased base pair separation caused by complexation with the guest. 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

Figure 1. Schematic representation of remodelling mechanisms. (Adapted form Langst and Becker, 2004.) The schemes show nucleosomes from the top. (a) The twist diffusion model - Twisting of DNA moves it over the histone surface in one base pair increments. This changes the position of the DNA with respect to the histone, as shown by the open and closed circles, (b) The Loop recapture model - Extranucleosomal DNA is pulled into the nucleosomes to replace a DNA segment which consequently loops out. This loop is then propragated over the histone surface like ripples of a wave. The star,, indicates how this leads to a change in the position of DNA relative to the nucleosome. (See Colour Plate 4.)...

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

Figure 10.7. Schematic representation of the Rev protein, emphasizing its two key functional domains. The secondary structure of the RRE, highlighting the Rev biding site, is shown. Residues essential for RRE are in bold. The intervening bulge contains two non-Watson-Crick base pairs, G48 G71 and G47 A73, and a bulged base U72. ...

The preceding approach can be viewed as an orbital representation analogue for a recently proposed Kohn-Sham-based pair-density functional theory [17],... 

C) Schematic representation of L form of E. coli. tRNAcys. Some tertiary base pairings are indicated by dashed lines. No modified bases are shown. See Hou et al,180... 

Figure 5.19 Schematic representation of the two strands of a nucleic acid. P = phosphate and S = sugar bases are as in Figure 5.18. The two strands of the double helix are held together through specific hydrogen bonds (base pairing)...

Solvent-accessible surface representation of the GlnRS enzyme complexed with tRNA and ATP. The region of contact between tRNA and protein extends across one side of the entire enzyme surface and includes interactions from all four protein domains. The acceptor end of the tRNA and the ATP are seen in the bottom of the deep cleft. Protein is inserted between the 5 and 3 ends of the tRNA and disrupts the expected base pair between Ul and A72. (From M. G. Rould, J. J. Persona, D. Soil, and T. Steitz, Structure of E. coli glutamyl-tRNA synthetics complexed with tRNA ln and ATP at 2.8-A resolution, implications for tRNA discrimination, Science 246 1135-1142, 1989, 1989 by the AAAS.)... 

Fig. 41. Schematic representation of the columnar triple-helical superstructure derived from the X-ray data for (LP2, LU2) each spot represents a PU or UP base pair spots of the same type belong to the same supramolecular strand the dimensions are compatible with an arrangement of the PTP and UTU components along the strands indicated (see also text) the aliphatic chains stick out of the cylinder, more or less perpendicularly to its axis a single helical strand and the full triple helix are respectively represented at the bottom and at the top of the column [9.152].

In Figure 16.15 we show a schematic representation of the duplex formed from d(GAATTC). Bases from one monomer pair with those from a second to form the duplex. G forms base-pairs with C, and A with T through hydrogen bonding. These base-pairs are referred to as Watson-Crick base-pairs, and they make up the rungs of the ladder associated with the familiar double helix of DNA. 

Figure 16.15 A schematic representation of a duplex formed from the self-complementary monomer, d(GAATTC), that illustrates base-pairing and nearest-neighbor stacking interactions.

Figure 4. Detailed molecular representation of the theoretically predicted base stacking and base pairing of A (single lines) and T (solid lines) bases in the low energy w a = 105°, 115° helix of Figure 3. The view is drawn perpendicular to the helix axis represented by (- -).

Fig. 2 Schematic representations of two model duplexes composed of homopolymeric and alternating adenine-thymine base-pairs for clarity adenines are shown in green.

Overlap Geometry A schematic representation of the proposed overlap geometry for proflavine intercalated into a deoxy pyrimidine(3 -5 )purine site is presented below with the (o) symbols representing the location of the phenanthridine ring protons. The mutual overlap of the two base pairs at the intercalation site involves features observed in the crystal structures of a platinum metallointercalator miniature dC-dG duplex complex (55) and the more recent proflavine miniature dC-dG duplex complex (48), as well as features derived in a linked-atom conformational calculation of the intercalation site in the proflavine DNA complex (51). [4]... 

Figure 4 Schematic representation of DNase 1-DNA interactions. Approximately 10 base pairs (bp) of me DNA era in contact with DNase 1 on one side of the double helix (indicated in black). Side chains of DNase I residua interacting with the DNA we indicated. (Adapted Iron Ref. 26.)...

Fig. 2. Schematic representation of the DNA base pairs showing base and sugar numbering schemes, sugar puckers, and the location of the major and minor grooves...

Fig. 17. Schematic representation ofPtR Models 1-4 showing the C G/5 -G C base pairs as a function of slide and shift and how well CH(2 ) is shielded by 5 -G in each model. The 5 -G C base pair is on top. The arrows indicate the direction of positive shift and slide...

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