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Zoli M. Denaturation patterns in heterogeneous DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:051910. [PMID: 20866264 DOI: 10.1103/physreve.81.051910] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/10/2010] [Indexed: 05/29/2023]
Abstract
The thermodynamical properties of heterogeneous DNA sequences are computed by path-integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time-dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds between complementary strands. The portion of configuration space contributing to the partition function is determined, at any temperature, by selecting the ensemble of paths which fulfill the second law of thermodynamics. For a short DNA fragment, the denaturation is signaled by a succession of peaks in the specific-heat plots while the entropy grows continuously versus T. Thus, the opening of the double strand with bubble formation appears as a smooth crossover due to base pair fluctuation effects which are accounted for by the path-integral method. The multistep transition is driven by the adenine-thymine- (AT) rich regions of the DNA fragment. The base pairs path ensemble shows an enhanced degree of cooperativity at about the same temperatures for which the specific-heat peaks occur. These findings establish a link between microscopic and macroscopic signatures of the transition. The fractions of mean base pair stretchings are computed by varying the AT base pairs content and taking some threshold values for the occurrence of the molecule denaturation.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, CNISM, Università di Camerino, I-62032 Camerino, Italy.
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Benight AS, Gallo FJ, Paner TM, Bishop KD, Faldasz BD, Lane MJ. Sequence context and DNA reactivity. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1057-8943(96)80003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Otsuka J, Kunisawa T. Characteristic base sequence patterns of promoter and terminator sites in phi X174 and fd phage DNAs. J Theor Biol 1982; 97:415-36. [PMID: 6215541 DOI: 10.1016/0022-5193(82)90374-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hillen W, Unger B. Correlation of thermodynamic and genetic properties in the Tn10 encoded TET gene control region. Nucleic Acids Res 1982; 10:2685-700. [PMID: 6281740 PMCID: PMC320643 DOI: 10.1093/nar/10.8.2685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The thermal stability of the Tn10 encoded tetracycline resistance (TET) gene control region is investigated by melting studies using purified DNA restriction fragments containing various amounts of flanking sequences. In order to study the thermodynamic properties of this control region under conditions, where enough flanking DNA is present to mimic the situation in the chromosome, the five step melting process of a 1450-bp DNA fragment is analyzed. Because most of the sequence of this DNA is not known, the assignment of the melting transitions to segments of the DNA is done by an experimental method. This employs the preparation of subfragments from the 1450-bp DNA and comparison of their denaturation profiles with the one of the intact sequence. This approach results in the complete assignment of the five denaturation steps. Rather than from the ends, the unwinding starts from the TET gene control region in the middle of the 1450-bp sequence. A clear correlation between the thermodynamic and genetic properties of this DNA is observed. The regulatory sequence forms a small cooperative unit with the lowest stability in the entire fragment. The thermal denaturation of the TET repressor. TET operator complex reveals, that the TET repressor specifically recognizes the double stranded TET operator DNA and stabilizes this structure by 2.4 degrees C. This results is also discussed as an example of the possible action of denaturing or stabilizing proteins on this genetic control region.
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Yen WS, Blake RD. Analysis of high-resolution thermal dispersion profiles of DNA: Treatment as a collection of discrete subtransitions. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200607] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gotoh O, Tagashira Y. Locations of frequently opening regions on natural DNAs and their relation to functional loci. Biopolymers 1981; 20:1043-58. [PMID: 7225530 DOI: 10.1002/bip.1981.360200514] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200513] [Citation(s) in RCA: 195] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hillen W, Goodman TC, Wells RD. Salt dependence and thermodynamic interpretation of the thermal denaturation of small DNA restriction fragments. Nucleic Acids Res 1981; 9:415-36. [PMID: 6259627 PMCID: PMC326702 DOI: 10.1093/nar/9.2.415] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The influence of cation concentration on the thermal denaturation of DNA restriction fragments from the E. coli lac regulatory region and from pVH51, ranging in size from 43- to 880- bp, is described. Upon increasing the ionic strength, the melting transitions broaden in a cooperative manner at salt concentrations characteristic for the specific fragment. For three fragments studied in detail, the salt concentration dependence at the midpoint varied between 0.03 and 0.19 M Na+. Along with the broadening, the melting transitions become more symmetrical. This result is discussed with respect to the irreversibility of melting transitions at low ionic strength. After a cooperative broadening, the shape of the melting curves remains constant up to salt concentrations of 0.5 M Na+. The dTM/dlog[Na+] values for three fragments fall between 15.7 and 16.7. An easily applicable approximation of the van't Hoff equation is used to evaluate the enthalpies of 13 transitions arising from the denaturation of 43 to 600 bp. The results of this analysis are compared to calculations of the expected enthalpies based on calorimetric measurements. The TMs of most transitions were directly related to the base composition, but several deviations from the predicted behavior were observed. The possible influences of fragment length and sequence on the thermal stability are discussed. The experimental and mathematical procedure to resolve a thermal denaturation transition with a width f 0.17 +/- 0.01 degrees and its distinction from another preceeding transition only approximately 0.15 degrees away in an 880-bp Hae III fragment from pVH51 is described. This transition is about half as wide as the smallest one reported to date.
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Benight AS, Wartell RM, Howell DK. Theory agrees with experimental thermal denaturation of short DNA restriction fragments. Nature 1981; 289:203-5. [PMID: 6256654 DOI: 10.1038/289203a0] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Experimental melting transitions of several natural DNAs of known nucleotide sequences have recently been obtained. The differential melting curves of these DNAs-phi X174 DNA, fd DNA and SV40 DNA-all show distinctive sets of peaks or fine structure. Theoretical melting curves calculated from the sequences and a few a priori parameters have not accurately predicted the experimental transitions. Although calculated fine structure resembled experimental curves in some cases, the characteristic features of a DNA's differential melting curve could not generally be produced. Azbel and Gabbarro-Arpa et al. have recently obtained good agreement between calculated and experimental curves using a different theoretical approach-only ground-state configurations of DNA were considered for temperatures inside the transition region. Their results suggest that the basic model of DNA melting, common to all theoretical approaches, is accurate. We have used here an exact theoretical approach to calculated melting curves of four DNA restriction fragments of 95-301 base pairs containing the lactose promoter region (Fig. 1). Theoretical curves agree very well with the experimental transitions published by Hardies et al. and obtained in this laboratory.
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Wada A, Yabuki S, Husimi Y. Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1980; 9:87-144. [PMID: 6777116 DOI: 10.3109/10409238009105432] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fine structures which appear in the optical melting profile of DNA are examined from both the experimental and theoretical aspects. After a brief historical survey of the DNA melting experiments during the pre-fine-structure era in Section II, the high temperature-resolution experimental techniques which are essential to the investigation of fine structure are described in Section III. Then, the current status of the high-resolution study is reviewed first by a phenomenological description of the melting profile (Section IV) and then of the refolding profile (Section V), where a general idea about the cooperatively melting region and several factors affecting it is given. Sections VI and VII are devoted to the review of current theoretical works. Several well-established theoretical frameworks which correlate the base sequence with the melting phenomena are examined in terms of their rigorousness and usefulness. The molecular thermodynamic parameters concerning the DNA melting which have been evaluated by several research groups are compared and discussed. Finally, in Section VIII, current ideas on the correlation between the fine structure and genetic functions and genetic maps are reviewed. Some future problems relating to the fine structure are also discussed.
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Tong BY, Battersby SJ. Melting curves, denaturation maps, and genetic map of phiX174: their relations and applications. Biopolymers 1979; 18:1917-36. [PMID: 159080 DOI: 10.1002/bip.1979.360180808] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Funnell BE, Inman RB. Comparison of partial denaturation maps with the known sequence of simian virus 40 and phi X174 replicative form DNA. J Mol Biol 1979; 131:331-40. [PMID: 226718 DOI: 10.1016/0022-2836(79)90079-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Gotoh O, Wada A, Yabuki S. Salt-concentration dependence of melting profiles of lambda phage DNAs: evidence for long-range interactions and pronounced end effects. Biopolymers 1979; 18:805-24. [PMID: 435606 DOI: 10.1002/bip.1979.360180406] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Tong BY, Battersby SJ. Melting fine structure of ?X174 DNA and its fragments: A theroetical study. Biopolymers 1978. [DOI: 10.1002/bip.1978.360171213] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Vizard DL, White RA, Ansevin AT. Comparison of theory to experiment for DNA thermal denaturation. Nature 1978; 275:250-1. [PMID: 692704 DOI: 10.1038/275250a0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Steer WM, Molgaard HV, Bradbury EM, Matthews HR. Ribosomal genes in Physarum polycephalum: transcribed and non-transcribed sequences have similar base compositions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 88:599-605. [PMID: 689040 DOI: 10.1111/j.1432-1033.1978.tb12486.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The transcribed and non-transcribed sequences in Physarum polycephalum ribosomal DNA (rDNA) were separated by restriction nuclease digestion of pure rDNA and the products fractionated by zone sedimentation in sucrose gradients. The base compositions of the fragments were determined by analytical centrifugation in CsCl or in CsCl with netropsin. All the fragments had dA + dT contents in the range 44-48%. From the known sequence arrangement and transcription pattern of Physarum rDNA it was concluded that coding sequences, transcribed but non-coding sequences, and non-transcribed sequences all possess similar base compositions, contrary to the situation in many other systems. The thermal denaturation profile of Physarum rDNA is reported. It suggests the rDNA sequence is complex and supports the above conclusion of limited heterogeneity of base composition.
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Karataev GI, Permogorov VI, Vologodskii AV, Frank-Kamenetskii MD. Denaturation maps of DNA: experimental and theoretical maps of phiX174 DNA. Nucleic Acids Res 1978; 5:2493-500. [PMID: 566910 PMCID: PMC342179 DOI: 10.1093/nar/5.7.2493] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A formaldehyde denaturation map of the replicative form of phiX174 DNA is obtained. The RFI DNA was converted into a linear state by restriction endonuclease pst I which introduces into this DNA a single double-stranded break. The map has four clear-cut peaks. Their positions excellently correlate with the peak positions on the map of equilibrium denaturation theoretically obtained earlier from the known nucleotide sequence of phiX174 DNA. The sequence is also used for a calculation of the maps of smoothed AT-content. The maxima on these maps correlate well with the peaks on the denaturation maps. To reveal the causes of a good correlation between the experimental formaldehyde and theoretical equilibrium denaturation maps, the theoretical formaldehyde denaturation maps are calculated for different conditions (temperature, formaldehyde concentration) using the detailed theory of DNA interaction with formaldehyde developed earlier.
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Grachev MA, Perelroyzen MP. Measurement of the differential melting profile of a promoter-containing fragment of T7 DNA by means of a microspectrophotometer. Nucleic Acids Res 1978; 5:2557-64. [PMID: 673861 PMCID: PMC342185 DOI: 10.1093/nar/5.7.2557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A double-beam microspectrophotometer with a 5 microliter cell has been used to study denaturation of DNA in an aqueous solution. This instrument enables measurement of high-resolution differential melting profiles simultaneously at several wavelengths with 0.5 to 1 microgram of DNA. Therefore it becomes possible to study nucleic acids which are difficult to obtain in large amounts. The techniques have been employed to measure the differential melting profiles of T7 DNA and of a fragment of this DNA 1000 base pairs long which contains the four early promoters.
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Tachibana H, Wada A, Gotoh O, Takanami M. Location of the cooperative melting regions in bacteriophage fd DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 517:319-28. [PMID: 626741 DOI: 10.1016/0005-2787(78)90198-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Differential melting profiles of the linear replicative form (RF-III) DNA of bacteriophage fd, of the fragments obtained by the restriction endonuclease R.HinHI and of those obtained by R.Hga were investigated. With these results a physical map which locates the cooperative melting regions on the DNA was constructed, and compared with the genetic map.
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Lyubchenko YL, Vologodskii AV, Frank-Kamenetskii MD. Direct comparison of theoretical and experimental melting profiles for RF II phiX174 DNA. Nature 1978; 271:28-31. [PMID: 625323 DOI: 10.1038/271028a0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The determination by Sanger et al. of the comple nucleotide sequence for phiX174 DNA has made it possible for the first time to compare directly theoretical and experimental DNA melting profiles. The comparison shows that the theory predicts the observed shape of the differential melting curve surprisingly well. Calculation of the denaturation maps allows the peaks on the curve to be correlated with cooperative melting out of concrete regions on the sequence of nucleotides.
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