Polynucleotide circular dichroism calculations: Use of an all‐order classical coupled oscillator polarizability theory

Cech, Carol L.; Hug, Werner; Tinoco, Ignacio

doi:10.1002/bip.1976.360150110

Cited by 94 publications

(82 citation statements)

References 41 publications

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“…This interpretation agrees with the one preferred by Bush and Sclieraga [16], who assigned the shoulder in the C D spectrum near 230 nm to a weak 71 --f ?I* transition. Cech et al [21] place this band at 240 am in 3' AMP.…”

Section: Results a N D Discussionmentioning

confidence: 94%

“…about 90 in the dimer and trimer, increasing (1,21,31, 51 and 71 " C ) . The solid upper and lower curve in Fig.…”

Section: Chain-length Dqwndencementioning

confidence: 92%

“…Cech et al [21] attempted to calculate the C D of (dA)2 and (dA), in B-DNA geometry [22] and concluded that the measured C D of (dA), bears little resemblance to the calculated C D and it was suggested that B-like geometry might not appropriately describe the helical state of poly(dA). Finally, by far the most puzzling observation on the C D of poly(dA) thus far was first published by Greve et al [23], but not commented upon by these authors.…”

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confidence: 99%

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Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

Olsthoorn

Bostelaar

Rooij

et al. 1981

European Journal of Biochemistry

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The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA),,, n = 2, 3, 6, 9, 12, cxi, in aqueous solution was studied. The data were interpreted on the basis of a new conformational model for the stacked state suggested by our previous proton N M R studies on (dA)2 and (dA)3 Biochmz. 112, this model the stacked regions of the single-stranded oligomers consist of residues taking up a geometry resembling that of the B-DNA genus of structures (all sugars S or C2'-enrb) except those residues at the 3' end that do not 'feel' a following stacking interaction. The deoxyribose rings in the latter residues retain (or regain when melting out removes a stacking interaction somewhere along the chain) the conformational freedom (S N, N = C3'-endo) that these rings possess in the monomers 2'-deoxyadenosine 5'-methylphosphate or in 2'-deoxyadenosine 3',5'-bis(methylphosphate), as the case may be. It is shown that this model allows (a) construction of the C D spectra of (dA),, n = 3, 6, 9, 12, from those of the dimer and the polymer; (b) the separation of the weak C D displayed by the regular S-S stacking mode and the far stronger C D exhibited by the 3'-end S-N stacking (the latter C D resembles that of the A-DNA genus of structures); (c) delineation of the thermodynamics of stacking. The melting temperature remains constant and independent of chain length (about 50 "C) whercas AH" and AS" show a slight increase in absolute values on increasing n from 2 to x owing to small cooperativity effects. Near 0°C the dimer occurs for about 90% in the stacked form, the oligomers attain even higher conformational purities. It is suggested that premelting phenomena observed in the C D spectra of double-helical DNAs may also involve local transitions from the normal B-like ----S-S-S----stacking mode to an A-like ----S-S-N----stacking geometry.The correlation between the mode of pucker of the ribose (or deoxyribose) ring, the phosphate diester backbone conformation and vertical base-base stacking in oligonucleotides to form a specific type of single helix has been the subject of several studies conducted in our laboratory [l-91. We now present a conformational study of a series of oligodeoxyadenosine nucleotides (dA),, n = 2, 3, 6, 9, 12, a, (cf. Fig. 1) carried out by means of temperature-dependent circular dichroism. The reasons for this study are manifold; however, three main objectives may be discerned: (a) the need for a quantitative insight into the thermodynamics of stacking of single helices; (b) to find an explanation for the curious C D spectral properties displayed by poly(dA) at neutral pH, which in no way resembles that of the dimer (dA)2; (c) to explore a possible correlation between the C D properties and the unexpected conformational behaviour of (dA)z and (dAh recently discovered by means of NMR spectroscopy [7]. It was discovered that these three objectives This paper is part XVII in the series on Nucleic Acid Constituents from this laboratory; part XVI appeared earlier in this j...

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Section: Results a N D Discussionmentioning

confidence: 94%

“…about 90 in the dimer and trimer, increasing (1,21,31, 51 and 71 " C ) . The solid upper and lower curve in Fig.…”

Section: Chain-length Dqwndencementioning

confidence: 92%

mentioning

confidence: 99%

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Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

Olsthoorn

Bostelaar

Rooij

et al. 1981

European Journal of Biochemistry

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“…These assignments are identical to those used previously. 91 In the x-ray region, The polarizability was assigned to each point using absorption data from benzene. …”

Section: B the Polarizabilitymentioning

confidence: 99%

Polarized light scattering as a probe for changes in chromosome structure

Shapiro

1993

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“…In a relatively short period of time after their introduction, the macrocychc glycopeptide chiral selectors were used successfully in most chromatographic and electrophoretic methods including HPLC (1,2,7,9,(11)(12)(13)(14)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)29,(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(45)(46)(47)(48)(49)(50)(51)(52), [85][86][87][88][89] TLC (3), CE (4,5,8,10,15,52,61,69,…”

Section: Introductionmentioning

confidence: 99%

Enantiomeric separations using macrocyclic glycopeptide based chiral stationary phases, an application and mechanism study

Xiao¹

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Polynucleotide circular dichroism calculations: Use of an all‐order classical coupled oscillator polarizability theory

Cited by 94 publications

References 41 publications

Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

Polarized light scattering as a probe for changes in chromosome structure

Enantiomeric separations using macrocyclic glycopeptide based chiral stationary phases, an application and mechanism study

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