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Basepair

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. [Pg.441]

FIGURE 28.5 (a) Tube and (b) space-filling models of a DNA double helix. The carbohydrate-phosphate "backbone" is on the outside and can be roughly traced in (b) by the red oxygen atoms. The blue atoms belong to the purine and pyrimidine bases and lie on the inside. The basepairing is more clearly seen in (a). [Pg.1170]

Roth and Breaker1331 used in vitro selection to evolve DNA molecules of the type illustrated in Scheme 4, which self-cleave in the presence of histidine. (This is in principle mimicking a disabled mutant enzyme, of the sort mentioned in the introduction.1101) In this case a pool of 2 x 1013 modified DNAs was attached at the 5 -end, tightly but reversibly, to a solid support The polynucleotide was made up of a randomised sequence of 40 deoxynucleotides (N40 in Scheme 4) flanked by two regions of basepairing complementarity to the sequences on either side of a single upstream RNA linkage (rA). [Pg.346]

The chemistry of nucleic acid analogs has received much attention in recent years, and a series of nucleic acid models has been designed and widely prepared, in order to estimate and utilize their functionalities in relation to the specific basepairing properties ( J., i, ). These monomers and polymers, particularly those containing purines, pyrimidines, nucleosides, and nucleotides, are not only of interest to the field of heterocyclic organic chemistry, but also to that of biomimetic macro-molecular chemistry as synthetic analogs of the nucleic acids. [Pg.359]

At the 3 ends of both primers, there should be at least one CG-type basepair in any combination to facilitate complementary strand formation. [Pg.386]

Figure 3.25 Polymerase chain reaction. The steps involved in the chain reaction are as follows (i) Incubation of the DNA at a temperature above 90 °C in order to separate the two strands of the DNA duplex, (ii) Cooling of the solution to about 50 °C to allow annealing of the primers to the template (i.e. the nucleotides bind to the template DNA according to the basepairing rules), (iii) Finally, addition of the polymerase and Mg ions to extend the nucleotide primer and complete the synthesis of the complementary DNA, which takes place at about 70 °C. (iv) The sequence (i) to (iii) is repeated to allow another extension to occur many repetitions can be carried out which results in enormous multiplication of the DNA strands. NTPs - deoxyri-bonucleoside triphosphates. Figure 3.25 Polymerase chain reaction. The steps involved in the chain reaction are as follows (i) Incubation of the DNA at a temperature above 90 °C in order to separate the two strands of the DNA duplex, (ii) Cooling of the solution to about 50 °C to allow annealing of the primers to the template (i.e. the nucleotides bind to the template DNA according to the basepairing rules), (iii) Finally, addition of the polymerase and Mg ions to extend the nucleotide primer and complete the synthesis of the complementary DNA, which takes place at about 70 °C. (iv) The sequence (i) to (iii) is repeated to allow another extension to occur many repetitions can be carried out which results in enormous multiplication of the DNA strands. NTPs - deoxyri-bonucleoside triphosphates.
The structural variations can affect the width of the major groove, the extent of base stacking, as well as the tilt of the basepairs to each other. The local conformational changes are sequence dependent and can be intrinsic properties and thus permanent occurrences they can, however, also be induced by protein binding. The DNA sequence can thus serve a double purpose for the recognition between DNA and protein. [Pg.17]

Fig. I. (left) Baseparing between a guanine-cytosine basepair and coupling of the CO-stretch vibrations, (right) Linear infrared absorption spectra of CO-stretch region of the studied duplexes. Fig. I. (left) Baseparing between a guanine-cytosine basepair and coupling of the CO-stretch vibrations, (right) Linear infrared absorption spectra of CO-stretch region of the studied duplexes.
Traditional basepairing observed in first and second positions of codon tRNA mRNA... [Pg.435]

Figure 25-26 (a) Generalized representation of a tRNA molecule. Each segment represents a nucleotide, the actual number and sequence of nucleotides varies with the tRNA. There are regions of intrachain basepairing (dashed lines). The nucleotide at the long end has a ribose with a free 3 -OH. The nucleotide at the short end is phosphorylated at 5 -OH. The three nucleotides of the anticodon loop pair with the appropriate bases in mRNA. (b) Three-dimensional picture of a tRNA to show the manner in which the chain is coiled. An excellent review article on the determination of the structure of phenylalanine tRNA by x-ray diffraction has been published, J. L. Sussman and S.-H. Kim, Science 192, 853 (1976). [Pg.1279]

Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain. Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain.
The aminoacyl-tRNA s form polypeptide chains in the order specified by codons of the mRNA bound to the ribosomes (see Figure 25-28). The order of incorporation of the amino acids depends on the recognition of a codon in mRNA by the corresponding anticodon in tRNA by a complementary basepairing of the type A U and C G. The first two bases of the codon recognize only their complementary bases in the anticodon, but there is some... [Pg.1281]

Neutral molecules are carried between two organic phases through a water layer by water-soluble receptors containing a lipophilic cavity [6.40, 6.41]. Urea and nucleosides are transported using a metallocarrier [6.42a] and complementary basepairing agents [6.42b], respectively. [Pg.74]


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See also in sourсe #XX -- [ Pg.127 , Pg.129 , Pg.135 ]




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Basepair parameters

Guanine-cytosine basepair

Hoogsteen basepairs

Watson-Crick basepairing

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