Conformations and structural transitions in polydeoxynucleotides

Pilet, J.; Blicharski, J; Brahms, J.

doi:10.1021/bi00680a011

Cited by 97 publications

(56 citation statements)

References 34 publications

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“…Such strong base-base interactions give rise to intense CD spectra that are very sensitive to the overall solution conformation of these biomolecules. A number of reviews and books have appeared, during the last 30 years, specifically dealing with these topics [19][20][21][22]. Some clear correlations between a few characteristic CD spectral 4 features and the solution structure of various DNA molecules (B -DNA; A-DNA; C-DNA and so on) have been unambiguously established.…”

Section: Introductionmentioning

confidence: 99%

DOTAP/DOPE and DC-Chol/DOPE lipoplexes for gene delivery studied by circular dichroism and other biophysical techniques

Ciani

Casini

Gabbiani

et al. 2007

Biophysical Chemistry

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Cationic liposomes give rise to stable complexes with DNA molecules ( lipoplexes) that are of great interest for gene delivery applications. In particular, liposomes made up by a cationic lipid (DOTAP or DC-Chol) and a zwitterionic lipid (DOPE), produce stable adducts with single and double -stranded DNA oligonucleotides. Formation of these lipople xes has been further addressed here by circular dichroism spectroscopy (CD) and by other independent biophysical methods. Titration of DNA oligonucleotides with cationic liposomes resulted into significant modifications of their circular dichroic bands. Such spectral modifications were ascribed to progressive DNA condensation and loss of native conformation, as a consequence of the electrostatic interactions taking place between the phosphate groups of DNA and the positively charged head groups of cationic lipids. In all cases, the loss of the CD features characteristic of the native DNA conformation closely matched the inflection point of zeta potential profiles. The resulting adducts showed peculiar and non-canonical CD spectra, while exhibiting appreciable stability at physiological pH.

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Section: Introductionmentioning

confidence: 99%

DOTAP/DOPE and DC-Chol/DOPE lipoplexes for gene delivery studied by circular dichroism and other biophysical techniques

Ciani

Casini

Gabbiani

et al. 2007

Biophysical Chemistry

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“…It has been shown previously that differences in the conformation of the phosphate-ribose backbone, and particularly in the orientation of the phosphate groups and in conformational transitions, characterize synthetic DNAs composed of different base sequences (4). Thus, it has been found that the alternating polynucleotide poly [d(A-T)l undergoes a structural transition to the A form, whereas the double stranded homopolymer poly [d(A)].…”

Section: Introductionmentioning

confidence: 99%

“…poly [d(T)3 cannot adopt the A form (4)(5). It was thus proposed that the alteration of the backbone conformation as a consequence of different base sequences may have an important role in DNA recognition and protein interaction (4)(5)(6).…”

Section: Introductionmentioning

confidence: 99%

Conformation of DNA in chromatin reconstituted from poly [d(A-T)] and the core histones

Brahms¹,

Brahmachari²,

Angelier³

et al. 1981

Nucl Acids Res

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Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly fd(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation close to C3'-endo puckering is detected in the Raman spectra. In addition, the circular dichroism (C.D.) spectra of reconstituted chromatin with poly PI(A-T)j exhibits an increased intensity at about 262 nm.A second feature acquired by poly rd(A-T)l in nucleosome formation from core histones is related to the presence of a negative band at about 280 nm in the C.D. spectra. The nature of this change is correlated with a DNA conformation characterized by a decreased number of base pairs per turn (28,29). This indicates that these two features of reconstituted nucleosomes reflect the presence of two types of DNA conformations, which overall form is of the B type (22,36).

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“…Information on conformational fluctuations in DNA is also of interest in connection with the use of spectroscopic tools (circular dichroism, infrared, Raman) to deduce the average conformational state of DNA (13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

1H nuclear magnetic resonance investigation of flexibility in DNA.

Early¹,

Kearns²

1979

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

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In this paper we report successful observations of proton NMR spectra of native double helical salmon sperm and calf thymus DNA of various lengths. Measurements of the linewidths arising from proton-proton dipolar interactions are used to obtain information about the dynamic behavior of DNA helices in solution. Depending upon which protons are used to monitor the local internal motions of the DNA, different results are obtained. The lowfield resonances from hydrogen-bonded imino protons in the base pairs indicate that the correlation time for reorientation of base pairs is less than 3 X 10-7 sec, whereas correlation times for motion of neighboring sugar protons relative to the aromatic protons are <5 X 10-8 sec for DNA that is over 200 base pairs long. These observations indicate that there is considerably more internal flexibility in the DNA molecules, especially in the backbone, than is indicated by classic hydrodynamic studies of DNA.The determination of the conformational state and the flexibility of DNA is of considerable interest in connection with studies of the hydrodynamic properties of DNA (1-4), the structure of DNA in chromosomes (5-8), the folding of DNA in phage particles (9), supercoiling in circular DNA (10, 11) and linear DNA (12), and computations of superhelical structure and energetics of DNA foldings (5-8, 10, 11). Information on conformational fluctuations in DNA is also of interest in connection with the use of spectroscopic tools (circular dichroism, infrared, Raman) to deduce the average conformational state of DNA (13)(14)(15).NMR spectroscopy is an excellent tool for studying flexibility in large molecules. Some preliminary 31P NMR studies of high molecular weight calf thymus DNA and chromatin (16) and nucleosome core particles have been reported (17,18), and these indicate there is considerable flexibility in the backbone (linewidths of 20-50 Hz). Previous attempts to use 1H (19) and '3C (20) NMR on native DNA were unsuccessful. Patel has successfully studied the 'H NMR of simple sequence synthetic DNA (21,22), but these molecules are believed to be unusually flexible due to formation of branched duplex regions and hairpins and therefore may not be good models for studying flexibility in native DNA. In 1977, we demonstrated (23) that it is possible to obtain partially resolved NMR spectra on high molecular weight native double-helical DNA, and in the present paper we have used NMR and the fact that NMR linewidths and relaxation times are sensitive to local internal motions to detect flexibility in the DNA that is not evident when the DNA is studied by other classical techniques.Our results show that it is possible to obtain useful proton NMR spectra on DNA of unexpectedly high molecular weight and make possible a number of applications of NMR to the study of DNA properties in solution. EXPERIMENTAL Salmon sperm (or calf thymus) DNA (Worthington) was dissolved (10 mg/ml) in 100 ml of 0.1 M NaAcO/2 mM ZnCl2 at pH 4.6, and S1 nuclease (1000 international units) was added. This so...

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Conformations and structural transitions in polydeoxynucleotides

Cited by 97 publications

References 34 publications

DOTAP/DOPE and DC-Chol/DOPE lipoplexes for gene delivery studied by circular dichroism and other biophysical techniques

DOTAP/DOPE and DC-Chol/DOPE lipoplexes for gene delivery studied by circular dichroism and other biophysical techniques

Conformation of DNA in chromatin reconstituted from poly [d(A-T)] and the core histones

1H nuclear magnetic resonance investigation of flexibility in DNA.

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