Secondary Structure of DNA depends on Base Composition

Bram, Stanley

doi:10.1038/newbio232174a0

Cited by 115 publications

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“…Recently, a relatively rapid technique to fractionate and sequence large pyrimidine oligonucleotides has been developed; the sequences of long pyrimidine tracts in fd DNA of [9][10][11][12][13][14][15][16][17][18][19][20] base residues have been determined (6). In this report, the sequences of the large pyrimidine products from fl and OX174 DNA are presented.…”

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Pyrimidine Sequences from the DNA of Bacteriophages fd, fl, and ϕX174

Ling

1972

Proc. Natl. Acad. Sci. U.S.A.

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By the use of techniques previously developed to determine the sequence of large, unique pyrimidine oligonucleotides in bacteriophage fd DNA, pyrimidine sequences in the related phage fl and the unrelated phage 4X174 amber 3 were determined. The DNA of fl contains many pyrimidine sequences completely identical to those in fd, including one sequence of 20 Recently, a relatively rapid technique to fractionate and sequence large pyrimidine oligonucleotides has been developed; the sequences of long pyrimidine tracts in fd DNA of 9-20 base residues have been determined (6). In this report, the sequences of the large pyrimidine products from fl and OX174 DNA are presented. These sequences are compared with those previously obtained from fd DNA. MATERIALS AND METHODSThe techniques to fractionate and sequence large pyrimidine oligonucleotides from phage DNA were described in detail (6). The micro-methods of Sanger and coworkers (7-9) were used for the routine fractionation and identification of radioactive nucleotides.32P Fig. 1).Partial Digestions with Snake-Venom and Spleen Phosphodiesterase. Large oligonucleotides isolated from thin-layer chromatographs and previously dephosphorylated with bacterial alkaline phosphatase to remove their terminal phosphates were subjected to partial digestion with either snake venom or spleen phosphodiesterase (Worthington, Freehold, N.J.). The snake-venom phosphodiesterase was purified by the procedure of Laskowski (13). Digestions were performed in 5-IAI solutions, with an enzyme to substrate (weight) ratio of 1: 10, at 370 for 10-45 min, depending on the size and nature of the substrate. The digests were then spotted directly onto cellulose acetate strips for fractionation as described above.RESULTS AND DISCUSSION Fractionation of pyrimidine oligonucleotides Fig. la, b, and c show two-dimensional fractionations of the pyrimidine oligonucleotides obtained by the Burton depurination (12) of 32P-labeled fd, fl, and OX174 DNA, respectively. Studies (6) have shown that pyrimidine oligonucleotides separate according to their relative C:T content in the electrophoresis step, and according to their size in the chromatography step, to yield a very regular pattern of nucleotide spots. This regularity allows the accurate prediction of the composition of a pyrimidine oligonucleotide by its position on the thin-layer plate. As seen in Fig. la, nucleotides containing only thymidine migrate relatively fast, and those containing only deoxycytidine m'grate relatively slow in the electrophoresis step. With these two sets of nucleotides as reference points, it is possible to line up rows of nucleotides 742

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Pyrimidine Sequences from the DNA of Bacteriophages fd, fl, and ϕX174

Ling

1972

Proc. Natl. Acad. Sci. U.S.A.

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“…1 The data are from ref. 7. To a first approximation these ratios are related to the relative maximum intensity on the third layer line to that of the second layer line, but contributions from other layer lines are expected to increase the intensity scattered near 10A from DNA solutions.…”

Section: Resultsmentioning

confidence: 99%

“…[A short preliminary report of three high-humidity patterns has recently been published (6)]. The high-humidity experiments presented here were prompted by the finding that the wide-angle x-ray scattering patterns of natural and synthetic DNAs in solution were, indeed, functions of the nature of the DNA (7). The wide-angle x-ray scattering patterns from all natural DNAs in solution show two intensity maxima near 13 and 10 A.…”

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“…However, the ratio of the intensity of the 10-maxima to the one at 13 A does not seem to vary, at least over the range 0.05-1 M monovalent salt. In the previous report (7), I stressed only the difference between DNA very rich in AT and typical or GC-rich DNA and declined to comment on the apparent differences between DNA very rich in GC and DNA moderately rich in AT because a sufficient number of experiments had not been done. After subsequent experiments with DNA of Microccus luteus and Escherichia coli, it became evident that the ratio of the 13-A to the 10-A maximum, and thus the ratio of the second to the third "layer line,"Y was a semi-continuous function of the AT content ( Table 1).…”

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“…The x-ray intensity corresponding to the first layer line is mostly obscured by the smallangle scattering of the whole molecule in solution. Nevertheless, the contribution from the first order bessel function term does raise the overall intensity scattered in the neighborhood of 20-30 A, and the relative intensity in this region was observed to be significantly larger for DNA very rich in AT (7). Abbreviation: r.h., relative humidity.…”

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Variation of Type-B DNA X-Ray Fiber Diagrams with Base Composition

Bram¹

1973

Proc. Natl. Acad. Sci. U.S.A.

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Eight natural DNAs of widely differing base composition have been studied by x-ray diffraction in fibers at high relative humidity. The resulting type B diffraction diagrams showed that all of the DNAs had a 34-A pitch and 3.4-A interbase pair separation. However, the intensity dlistribution on the inner three layer lines was a strong function of the base content. In diffraction diagrams of very AT-rich DNA, the intensity of the first and third layer line was 2-or 3-times stronger than in the patterns of GC-rich DNA. These high humidity diffraction patterns agree with x-ray scattering from solutions of DNA. The results are interpreted to imply that each AT base pair may have a different cross section than a GC pair. If this is so, it would appreciably alter the currently held ideas concerning DNA recognition.Until recently, it was generally accepted that DNA could exist only in one of three forms, and also that the structure of DNA was independent of the nature of the DNA. The latter conclusion was based on an x-ray fiber diffraction study of only the A forms of various natural DNAs (1). Nevertheless, x-ray fiber diffraction experiments on AT-rich DNAs at intermediate and low relative humidities (r.h.) have shown that the secondary structure under these conditions does depend on the base composition (2, 3) and that there exists at least several new forms for DNA.At high water contents, in fibers and in solution, calfthymus DNA exists in a conformation of the B type (4, 5). However, no extensive x-ray fiber diffraction study of the high-humidity configuration of various DNAs has been reported. [A short preliminary report of three high-humidity patterns has recently been published (6)]. The high-humidity experiments presented here were prompted by the finding that the wide-angle x-ray scattering patterns of natural and synthetic DNAs in solution were, indeed, functions of the nature of the DNA (7). The wide-angle x-ray scattering patterns from all natural DNAs in solution show two intensity maxima near 13 and 10 A. (Other maxima are observed at smaller equivalent Bragg spacings.) To a first approximation,. these maxima correspond to the maximum of the molecular transform of the fiber diffraction pattern on the second and third layer lines, respectively. The x-ray intensity corresponding to the first layer line is mostly obscured by the smallangle scattering of the whole molecule in solution. Nevertheless, the contribution from the first order bessel function term does raise the overall intensity scattered in the neighborhood of 20-30 A, and the relative intensity in this region was observed to be significantly larger for DNA very rich in AT (7). Abbreviation: r.h., relative humidity.It was also noticed that the sharpness of the 13-and 10-A maxima were functions of the base composition, but recenexperiments show that the width of these maxima is also aft fected by the salt content. However, the ratio of the intensity of the 10-maxima to the one at 13 A does not seem to vary, at least over the range 0.05-1 M...

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Investigation of DNA structural changes by infrared spectroscopy

1973

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SynopsisDNA-oriented samples of various origins were studied under different conditions of humidity and sodium chloride content by means of infrared spectroscopy.( 1 ) Oriented DNA ( M . Lysodeikticus, E. wli, calf thymus and salmon sperm) films a t 3-475 sodium chloride yield polarized infrared spectra which show drastic changes at relative humidities (r.h.) between 94% and O%, indicative of conformational changes:The measurements of the infrared dichroism a t frequencies of about 1230 cm-1 and a t about 1090 cm-1 allow one t o determine the orientation of the phosphate group, whereas the measurements at 1710 cm-1 characterize the base orientation. At humidities higher than 90% r.h. (B form) the bisector of OPO forms an angle of 70" relative to the helix axis, whereas at lower humidities, between 75% and 50% r.h. (A form) a rotation t o about 45" is observed. Simultaneously, the 0-0 line of phosphate group changes its orientation from 55" to 65" t o the helix when B + A transition takes place. The results are in general agreement with that of X-ray diffraction and allow one t o determine the orientation of the phosphate group with greater precision.( 2 ) The B-A conformational change is not observed for satellite DNA, isolated from Cancer pagums, of which the guanine + cytosine content is below 5%. As a function of decreasing humidities, one observes the transition:B form + disordered form A diagram of conformational changes of DNA's as a function of base composition and of r.h., suggests that B-A transition will occur for DNA of relatively higher G + C content, whereas for high (A + T ) content, base sequence may be of importance.The B-A transition is prevented in DNA at relatively high or very low sodium chloride content.

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Secondary Structure of DNA depends on Base Composition

Cited by 115 publications

References 15 publications

Pyrimidine Sequences from the DNA of Bacteriophages fd, fl, and ϕX174

Pyrimidine Sequences from the DNA of Bacteriophages fd, fl, and ϕX174

Variation of Type-B DNA X-Ray Fiber Diagrams with Base Composition

Investigation of DNA structural changes by infrared spectroscopy

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