Single-strand helix, modeling

While it is reasonable to assume that kinks are formed at the site of the covalent binding of BaPDE (34), it is also possible that such bends arise elsewhere on the double helix, due to the known formation of nicks and single-strand breaks (35,36). Therefore, the existence of kinks in the DNA helix at site I or site II binding sites should be further investigated, before such a model can be adopted definitively. 

With their model, Watson and Crick proposed that DNA replication begins with the unraveling of the double helix. Each single strand then serves as a template for the synthesis of its complementary strand. Free nucleotides are coupled to the single strand of DNA according to the rules of base pairing guanine +... 

The flexible helix modeled here is best described by the entire array of conformations it can assume. A comprehensive picture of this array is provided by the three-dimensional spatial probability density function Wn(r) of all possible end-to-end vectors (25, 35). This function is equal to the probability per unit volume in space that the flexible chain terminates at vector position relative to the chain origin 0,as reference. An approximate picture of this distribution function is provided by the three flexible single-stranded B-DNA chains of 128 residues in Figure 5(a). The conformations of these molecules are chosen at random by Monte Carlo methods (35, 36) from the conformations accessible to the duplex model. The three molecules are drawn in a common coordinate system defined by the initial virtual bond of each strand. For clarity, the sugar and base moieties are omitted and the segments are represented by the virtual bonds connecting successive phosphorus atoms. 

To predict the ion-dependent folding stability for a short DNA helix, we use a two-state model. Specifically, we assume that the conformational ensemble of the system consists of two states double-stranded (ds) helix as the folded state and single-stranded (ss) hehces (stabilized by the single-stranded self-stacking) as the unfolded state. For a given ionic condition... 

Although the chemical nature of single-stranded DNA was well known by 1950, it was Watson and Crick who finally solved the structure of double-stranded DNA in 1953 and proposed a double helix model of DNA based on x-ray diffraction data [2], This concept eventually earned them a Nobel prize in 1962. They proposed that DNA consists of two independent strands, each having alternate pentose sugar (deoxyribose) and phosphate units linked via ester linkage (phosphodiester) as part of their backbone... 

This K is considerably smaller than that of the single-strand polymer at neutral pH, and suggests that the molecules have a rather thick structure. Adopting the interrupted-helix model, we may apply Eq. (97) as in the case of poly-L-proline. Noting that the unit translation distance b0 is 1.70 A for the double-stranded Watson-Crick helix (263 ) [i. e., a distance of 3.40 A for two residues, one in each chain], and taking Mu = 328 for poly(adenylic acid), we obtain r = 22 residues per helical... 

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.. 

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