Double-helical template

If the rate-controlling step in the addition of each monomer to agrowing chain is, in all cases, assumed to be an enzymatically catalyzed chemical event rather than, for example, the unraveling of double helical template structure (in advance of the growing-chain end) where such exists, then the syntheses of DNA, RNA, and protein would, at first sight, all seem to represent similar, one-dimensional, stochastic processes. However, even... 

De Mendoza reported the first example of anion-directed helix formation in 1996 [91]. The assembly of this helical structure relies, not only on electrostatic interactions between the anionic template and the positively charged strands, but also on hydrogen bonding. The tetraguanidinium strand 69 (see Scheme 34) self-assembles around a sulfate anion via hydrogen bonding to produce a double helical structure. The formation of this assembly and its anion-dependence was proposed on the basis of NMR and CD spectroscopic studies. 

Replication of DNA is an enzymatic process that starts with the partial unwinding of the double helix. Just before the cell division, the double strand begins to unwind. As the strands separate and bases are exposed, new nucleotides line up on each strand in a complementary fashion, A to T, and C to G. Two new strands now begin to grow, which are complementary to their old template strands. Two new identical DNA double helices are produced in this way, and these two new molecules can then be passed on, one to each daughter cell. As each of the new DNA molecules contains one strand of old DNA, and one new, the process is called semiconservative replication. 

The double-helical DNA molecule contains an internal template for its own replication and repair. 

Coding of a Polypeptide by Duplex DNA The template strand of a segment of double-helical DNA contains the sequence... 

The replication of DNA Double helix of DNA unwinds. Each single strand serves as a template for the formation of a new DNA strand containing the complementary sequence. Two daughter double helices are formed, each containing one of the parent strands. 

A number of helical and double-helical complexes have been obtained with polypyridine ligands, which bind various metal ions yielding helical and double-helical [9.70-9.74] complexes that present interesting redox and metal-metal interaction properties [9.75]. The graphs of the double-helicates represent braids based on two threads and several crossings [9.1,9.76], that may serve as templates for the synthe-... 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Figure 2. The logic of complementary replication and mutation. Template-induced synthesis of RNA is based on nucleotide complementarity (G h C and A = U) in the double helix. The synthesis starts at the 5 -end of the template and adds nucleotide after nucleotide to the growing chain. In this way a negative copy is obtained, being the minus- or plus-strand when a plus- or a minus-strand was the template, respectively. Dissociation of the double-helical plus-minus-duplex completes complementary replication. Three classes of...

PCR works by the synthesis of two short oligonucleotides that bind correctly to opposite strands of the DNA to be replicated. This allows the DNA polymerase enzyme to begin to assemble copies of the two strands, resulting in two new DNA strands. Heating the sample causes the unwinding of the resulting double helices and provides four fresh strands that can be used as the templates for the formation of four more strands. The procedure is repeated 20-60 times over the course of a few hours either... 

The double-helical structure of DNA and the ability of the molecule to unravel in order to template the formation of copies of itself and transcribe RNA is clearly connected intimately with the supramolecular interactions that bind the two nucleotide strands together. It is the information encoded within the individual nucleobases that tells the molecule to form a double helix. This is an... 

The self-assembling double-helical structure of DNA has provided the inspiration for a further area of supramolecular self-assembly, namely the use of metal ions to template the assembly of organic threads into... 

The scope of synthetic higher knots is relatively limited at present because of the tremendous synthetic challenges involved. However, we have already seen that natural system forms knots readily and DNA is a particular good candidate as a knot template because of its double helical nature. The knot-forming tendencies of DNA have been exploited particularly by the group of Nadrian C. Seeman (New York, USA) to produce by design using both self-assembly and deliberate manipulation (e.g. by... 

Each chain of double-helical DNA is bound to the other through complementary base pairs, with adenine (A) in one being hydrogen-bonded to thymine (T) in the other, and guanine (G) to cytosine (C). Watson and Crick proposed that, to achieve precise copying of a nucleotide (base) sequence, the two chains of the DNA must unwind from one another to allow each single chain to act as a template for the synthesis of a new one. Thus, the assembly of the sequence in the newly synthesized... 

Other DNA polymerases are known. DNA polymerase II and III are produced by the poZB and dnaA genes of E. coti They are similar to DNA polymerase I in most properties. They differ however, in template preferences. While DNA polymerase I acts best to fill in extended single-stranded regions near double-helical regions, DNA polymerases II and III act optimally on double-stranded DNA templates that have short gaps. 

Template strand (Section 28.4) The strand of double-helical DN.4i that does not contain the gene. 

Reports of double-helical complexes have appeared in the literature since the sixties. Despite the early interest, it is only more recently that emphasis has been given to the use of metal template synthesis for obtaining a wide range of doubly-and triply-stranded systems. In part, this attention has had its origins in an early report by Lehn et al. in which the spontaneous assembly of a dicopper(I)-containing double helix was described. 

The double-helical model of DNA and the presence of specific base pairs immediately suggested how the genetic material might replicate. The sequence of bases of one strand of the double helix precisely determines the sequence of the other strand a guanine base on one strand is always paired with a cytosine base on the other strand, and so on. Thus, separation of a double helix into its two component chains would yield two single-stranded templates onto which new double helices could be constructed, each of which would have the same sequence of bases as the parent double helix. Consequently, as DNA is replicated, one of the chains of each daughter DNA molecule would be newly synthesized, whereas the other would be passed unchanged from the parent DNA molecule. This distribution of parental atoms is achieved by semiconservative replication.. 

It unwinds a short stretch of double-helical DNA to produce a single-stranded DNA template from which it takes instructions. 

Although RNA polymerase can search for promoter sites when bound to double-helical DNA, a segment of the helix must be unwound before synthesis can begin. A region of duplex DNA must be unpaired so that nucleotides on one of its strands become accessible for base-pairing with incoming ribonucleoside triphosphates. The DNA template strand selects the correct ribonucleoside triphosphate by forming a Watson-Crick base pair with it (Section 5.2.1). as in DNA synthesis. 

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