The analysis of circular dichroism spectra of natural DNAs using spectral components from synthetic DNAs

A procediure for the computation of the first neighbour frequencies of DNA's is presented. This procedure is based on the first neighbour approximation of Gray and Tinoco. We show that the knowledge of all the ten elementary CD signals attached to the ten double stranded first neighbour configurations is not necessary. One can obtain the ten frequencies of an unknown DNA with the use of eight elementary CD signals corresponding to eight linearly independent polymer sequences. These signals can be extracted very simply from any eight or more CD spectra of double strafded DNA' s of known frequencies. The ten frequencies of a DNA are obtained by least square fit of its CD spectrum with these elementary signals. One advantage of this procedure is that it does not necessitate linear programming, it can be used with CD data digitalized using a large number of wavelengths, thus permitting an accurate resolution of the CD spectra. Under favorable case, the ten frequencies of a DNA (not used as input data) can be determined with an average absolute error < 2%. We have also observed that certain satellite DNA's, those of Drosophila viriZis and CalZinectes sapidus have CD spectra compatible with those of DNA's of quasi random sequence ; these satellite DNA's should adopt also the B-form in solution. INTRODUCTIONThe dependence of CD spectra on base composition has been extensively studied during the past ten years. Felsenfeld and Hirschmann1 have first investigated linear dependence of UV absorption spectra over GC content these authors have concluded to the insufficiency of such an hypothesis. ORD

Section: Resultsmentioning

confidence: 99%

A simple method for the computation of first neighbour frequencies of DNAs from CD spectra

Marck

Guschlbauer²

1978

“…Therefore, the altered CD may be interpreted to reflect a structural change of the DNA induced by complex formation with the TET repressor. The positive CD band of nucleic acids in particular is interpreted to be very sensitive to the local structure of DNA [19,20].…”

Section: _7mentioning

confidence: 99%

TET repressortetoperator complex formation induces conformational changes in thetetoperator DNA

Atschmied

Hillen

1984

The structural changes of the tet operator DNA upon binding of the TET repressor protein are examined by circular dichroism. For this purpose a 70 bp DNA fragment was prepared which contains both tet operators. About 67% o'f the base pairs of this DNA are involved in specific interaction with the TET repressor.A rather large change in the CD of the DNA is induced by binding of the TET repressor. The shape of the CD difference spectrum is similar to the respective difference found for the lac operator DNA upon complex formation with the lac repressor. However, the effect induced by the TET repressor on tet operator DNA seems to comprise both the specific and non-specific effect of the lac repressor on the structure of DNA [Culard, F. and Maurizot, J.C. (1981) Nucl. Acids Res. 9, 5157-5184]. Specificity of binding is confirmed by the lack of any effect of the TET repressor on the CD of a 95 bp lac operator containing DNA fragment, by the reduced mobility of TET repressor-tet operator complexes on polyacrylamid gels under CD conditiones, and by a titration experiment of tet operator DNA with TET repressor employing the CD change. The latter experiment reveals a stoichiometry of four TET repressors per tet operon control region.

“…The strong similarity between spectra indicates that the 16-mer is present as a B-fonm duplex. The small differences in peak shape and amplitude are likely to reflect differences in base composition (22) and sequence (23,24) (20). Subject to the assumption that a single CAP dimer excludes others from binding to the same region of DNA, this value is a measure of the length of the DNA binding site.…”

Section: ' -T G T G a G T T A G C T C A C U A C A C T C A A T C G A Gmentioning

confidence: 99%

CAP binding to B and Z forms of DNA

Fried

Crothers

1983

We have examined the interaction between the cyclic AMP receptor protein (CAP) and a small DNA fragment containing its specific recognition sequence by circular dichroism spectroscopy. The binding of CAP to this fragment induces a B to "C-like" change in the CD spectrum, which is different from that observed for non-specific binding. A one-to-one (CAP dimer to DNA) binding stoichiometry was deduced from spectroscopic titration data, as was a non-specific binding site size of 17 bp/dimer. In addition, we have compared the non-specific binding affinity of CAP for the B and Z forms of synthetic DNA copolymers. A slight preference for the B form was found. These results do not support the recent specific suggestion that CAP binds to a left-handed form of DNA (1), but indicate more generally that an optically detectable conformational change takes place in DNA on binding CAP.