DNA base pairs

Figure 9.19 Nucleotide sequence of the 21-base pair DNA fragment cocrystalUzed with the DNA-binding domain of p53. The p53 binds in a sequence-specific manner to the shaded region.

Backbone (protein), 1028 Backside displacement. reaction and.363-364 von Baeyer, Adolf, 113 Baeyer strain theory, 113-114 Bakelile, structure of, 1218 Banana, esters in, 808 Barton, Derek, H. R., 389 Basal metabolic rate, 1169 Basal metabolism. 1169-1170 Base, Bronsted-Lowry, 49 Lewis, 57, 59-60 organic, 56-57 strengths of, 50-52 Base pair (DNA), 1103-1105 electrostatic potential maps of. 

Fig. 13. Images of 168-base-pair DNA minicircles in 1 mM MgCl2 (a) and 1 mM ZnBr2 (b), showing a factor of 4 increase in kink density inZn2. Reproduced with permission from Ref. (46). Copyright 1997, Nature (London).

Fig. 6 Dynamic molecular motions can gate DNA-mediated charge transport. Two time constants (5 and 75 ps) are observed for hole transfer from photoexcited ethidium, tethered and intercalated near the end of a 14-base pair DNA duplex, to a base analog, 7-deazaguanine, in DNA. The 5 ps time constant, which is independent of distance between 10-17 A, is due to direct hole transfer, while the 75 ps time constant corresponds to reorientation of the ethidium before hole transfer. Adapted from [96]... 

Sequence tagged site (STS) Short (200-500 base pairs) DNA sequence that has been identified and located as a single occurrence in the human genome. Detectable by polymerase chain reaction, STSs are useful for localizing and mapping of sequence data reported from different laboratories (see also expressed sequence tags). 

As to the stoichiometry of the H3-H4-DNA particle, two complexes were identified an H3-H4 tetramer and an H3-H4 octamer, each associated with about 140 base pairs of DNA. The complexing of 140 base pairs of DNA with H3 and H4 resulted in the formation of nucleosome-like particles, as observed by the EM, and reported to have an s20base pairs (Bina-Stein and Simpson, 1977 Bina-Stein, 1978). These results differ from those of Simon et al. (1978) who report that at least two complexes of H3 H4-DNA can be obtained upon reconstitution of H3, H4, and 150 bp DNA. In this experiment both an octamer and a tetramer of H3-H4 were found bound to 150 base pairs of DNA, having sM,w equal to 10.4 and 7.5 for the octamer and tetramer, respectively. The stoichiometry of the complexes obtained is dependent on the histone-to-DNA ratio. At low ratios of histone to DNA the predominant species contains an H3-H4 tetramer per 150 base pairs of DNA. At a histone-to-DNA ratio of 1 1 the octamer prevails. The nuclease and protease digestion experiments (Camerini-Otero et al., 1976 Sollner-Webb et al., 1976) were performed at a histone-to-DNA ratio of 0.5, conditions which for 140-base-pair DNA would lead primarily to a tetrameric complex. Therefore, it seems that a tetramer of H3 H4 is sufficient for the generation of nuclease-resistant fragments similar to those of complete nucleosomes. Upon addition of H2A and H2B to the tetrameric complex, nucleosomes are formed. Addition of H3-H4 to the tetrameric complex resulted in an octameric complex which is similar in compaction to nucleosomes. H3-H4 tetramers and octamers were similarly found complexed with about 140 base pairs of DNA upon reconstitution of H3-H4 with SV40 DNA. Both complexes were reported to be able to fold 140 base pairs of DNA (Thomas and Oudet, 1979). 

Figure 20.14 Preparation for DNA replication. At Least three proteins are involved DNA helicases disrupt hydrogen bonds between bases to allow the two strands to unwind single-strand DNA-binding proteins stabilise the unbound strands in preparation for base pairings DNA topoisomerase relaxes strain in the strands to facilitate polymerisation.

Allison, S.A., Sorlie, S.S., and Pecora, R. (1990) Brownian dynamics simulations of wormlike chains Dynamic light scattering from a 2311 base pair DNA fragment. Macromolecules 23, 1110-1118. 

Fig. 16 AFM images of 168 base-pair DNA minicircles in a 1 mM MgCh and b 1 mM ZnBr2, showing a fourfold increase in kink density in Zn ". Selected molecules are displayed magnified by a factor of four to the left of each image [123]. Reprinted with permission...

Figure 5-53 (A) JH NMR spectrum of a 17 base-pair DNA segment from the operator sequence OR3 from bacteriophage X in D20 at 37°C. (B) Combined COSY above the diagonal and NOESY (below the diagonal) spectra. C5H and C6H J coupling is established from cross-peaks in box d for cytosines and in box a for thymines. Two unresolved cross-peaks give rise to the more intense spots marked by arrows. Box b contains cross-peaks from scalar coupling of the two H2 protons to the HT protons of the deoxyribose rings. Most of the aromatic proton resonances could be assigned using the NOE cross-peaks in box f. For further details see Wemmer et al.676 See also Bax and Lerner.672 Courtesy of B. Reid.

The broad peaks B, D, and E are shifted far upfield by reaction with bisulfite (Eq. 5-11) suggesting that they are not hydrogen bonded and are present in the loop of the stem-loop structure. Peaks A, E, F, and G correspond to resonances 64, 7, 67, and 4, respectively, in (A) and represent fluorouracil in the stem structure. From Chu et al.69i Courtesy of Jack Horowitz. (C) A 31P NMR spectrum of a synthetic 14 base-pair DNA segment related to the E. coli lac operator. The palindromic sequence is TCTGAGCGCTCAGA. The numbers refer to the positions from the 5 end. From Schroeder et al.688... 

Different conformations of base-paired DNA (a) the untwisted straight ladder, (b) the normal spiral ladder. The stepladder structure is unstable it can be converted into a spiral ladder by a right-handed twist, a change that permits the planes of the base pairs to come into close contact. 

Stuart, G.W., Searl, P.F., Chen, H.Y., Brinster, R.L. and Palmiter, R.D. (1984) A 12-base-pair DNA motif that is repeated several times in metallothionein gene promoters confers metal regulation to a heterologous gene. Proc. Natl. Acad. Sci. USA, 81, 7318-7322. 

Dicerium complex 24 took 24 h at 37 °C or 5 h at 55 °C to yield hydrolysis products of a 192-base pair DNA [60], Conversely, PCD-based Co(m)Cyc derivatives degraded the linear DNA duplex into small fragments in a few hours at 25 °C. The facile DNA hydrolysis by the PCD-based Co(m)Cyc was due to the activation of Co(m)Cyc upon attachment to PCD rather than to cooperation among two or more catalytic centers or facilitation of complex formation between DNA and the PCD-supported catalyst. 

Oberle I, Rousseau F, Heitz D, et al. Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome. Science 252 1097-1102,1991. 

Keywords Cytosine, Guanine, Watson-Crick Base-Pair, DNA Oligomers, Conical Intersection,... 

Figure 1. Sketch of the complex of the five-finger human GLI protein with a 21-base pair DNA fragment. (Reproduced with permission from reference 20. Copyright 1993 American Association for the Advancement of Science.)...

In the crystal structure [711], a dimes formed by two N-terminal 434 repressor fragments is bound to the 20 base pairs DNA duplex so that the complex has overall 2-fold rotational symmetry. The polypeptide chain is folded into five a-helices HI to H5, with helices H2 and H3 forming the helix/turn/helix motif (Fig. 20.16). Helices H3 and H3 of the 434 repressor dimer insert into two successive major grooves of the operator DNA whereas the N-termini of the flanking helices H2, H4 and H2 H4 contact the sugar-phosphate backbones. 

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