Stability distribution in the phage lambda-DNA double helix: a correlation between physical and genetic structure.

Statistical analyses on the positional correlation of physical-stability and base-sequence distribution maps with genetic map are made for the whole DNA (48502 bases) of lambda-phage. The susceptibility to a double-helix unfolding perturbation and the fraction of the transient opening of a particular region of the double helix are adopted to define this physical stability. The principal features obtained are: A) The DNA double strand of protein coding regions is found to have homostabilizing propensity around a defined stability which is characteristic to each individual gene. B) The stability of the double helix in non-protein coding region fluctuates, on average over the whole region, more than that in protein coding region. C) Boundary regions of protein coding and non-protein coding regions are regions of high stability-fluctuation. Stability especially fluctuates at the protein-coding-region side of the boundary. Contrary to the quiet feature of the interior part of protein coding region rather noisy part exists at its edge. D) One frequently opening region coincides with the attaching site for the site specific recombination between phage and bacterial DNA. There are two possible ways to explain the noisy feature in the stability distribution in non-protein coding regions: 1) The region has been used as the locus of recombination as evolution took place. Thus DNAs which were homostabilized around a different value characteristic to each individual DNA, have been joined there many times, so that the noise has accumulated as a remnant of evolutional history; and/or 2) the base-composition homogenizing or double-helix homostabilizing mechanism does not work in unneeded region such as non-protein coding region or introns. Since corresponding characteristics have been found in our previous analyses on other viral and globin-gene DNAs, the rules mentioned above may be comprehensively extended to other DNAs.

[1]  Akiyoshi Wada,et al.  Spectral analysis on the melting fine structure of λ DNA and T2 DNA , 1977 .

[2]  P. V. von Hippel,et al.  DNA-protein interactions. , 1972, Annual review of biochemistry.

[3]  B. Funnell,et al.  Comparison of partial denaturation maps with the known sequence of simian virus 40 and phi X174 replicative form DNA. , 1979, Journal of molecular biology.

[4]  A. Wada,et al.  Stability mapping along the DNA double strand and its relation to the genetic map. , 1979, Journal of biochemistry.

[5]  B. Y. Tong,et al.  Comparison of theoretical denaturation maps of phiX174 and SV40 with their gene maps. , 1979, Nucleic acids research.

[6]  Yusaku Tagashira,et al.  Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles , 1981 .

[7]  Fisher Lm.  DNA unwinding in transcription and recombination. , 1982 .

[8]  M. Fixman,et al.  Theory of DNA melting curves , 1977, Biopolymers.

[9]  J. Otsuka,et al.  Characteristic base sequence patterns of promoter and terminator sites in phi X174 and fd phage DNAs. , 1982, Journal of theoretical biology.

[10]  W. Szybalski,et al.  A comprehensive molecular map of bacteriophage lambda. , 1979, Gene.

[11]  B. Y. Tong,et al.  Melting curves, denaturation maps, and genetic map of ϕX174: Their relations and applications , 1979, Biopolymers.

[12]  G. Matsuda,et al.  The light chains of muscle myosin: its structure, function, and evolution. , 1983, Advances in biophysics.

[13]  O. Gotoh,et al.  Prediction of melting profiles and local helix stability for sequenced DNA. , 1983, Advances in biophysics.

[14]  S. Stirdivant,et al.  DNA structure and gene regulation. , 1980, Progress in nucleic acid research and molecular biology.

[15]  J. Brahms,et al.  Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. , 1980, CRC critical reviews in biochemistry.

[16]  N. Sueoka.  Variation and heterogeneity of base composition of deoxyribonucleic acids: A compilation of old and new data , 1961 .

[17]  S. Miyazawa,et al.  Relationship between mutability, polarity and exteriority of amino acid residues in protein evolution. , 2009, International journal of peptide and protein research.

[18]  J. Champoux.  Proteins that affect DNA conformation. , 1978, Annual review of biochemistry.

[19]  Y. Lyubchenko,et al.  Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde. , 1976, Journal of molecular biology.

[20]  O. Gotoh,et al.  Locations of frequently opening regions on natural DNAs and their relation to functional loci , 1981, Biopolymers.

[21]  Janet M. Thornton,et al.  Conformation of terminal regions in proteins , 1982, Nature.

[22]  A. Wada,et al.  "Thermal stability" maps for several double-stranded DNA fragments of known sequence. , 1978, Journal of biochemistry.

[23]  A. Wada,et al.  Ligand‐induced melting reaction of specific‐sequence DNA molecules , 1982, Biopolymers.

[24]  A. Suyama,et al.  Correlation between Physical Stability Map and Genetic Map of DNA Double Strand , 1983 .

[25]  F. Sanger,et al.  Nucleotide sequence of bacteriophage lambda DNA. , 1982, Journal of molecular biology.

[26]  E. Freese.  On the evolution of the base composition of DNA , 1962 .

[27]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[28]  A Suyama,et al.  Correlation between thermal stability maps and genetic maps of double-stranded DNAs. , 1983, Journal of theoretical biology.

[29]  Y. Lyubchenko,et al.  Direct comparison of theoretical and experimental melting profiles for RFII ΦX174 DNA , 1978, Nature.