Oligonucleotide interactions. II. Differences in base stacking in linear and cyclic deoxythymidine oligonucleotides

Cantor, Charles R.; Fairclough, Robert H.; Newmark, Richard A.

doi:10.1021/bi00837a018

Cited by 25 publications

(16 citation statements)

References 27 publications

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“…One year later, cyclic oligonucleotides of uridine were also reported as a side product during the synthesis of uridine oligonucleotide . Optical studies of these circular oligonucleotides displayed quite different stacking manner from linear oligonucleotides . Later on, Ikehara et al.…”

Section: Artificial Cnasmentioning

confidence: 99%

Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topologycontrolled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.[a] Dr.

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Section: Artificial Cnasmentioning

confidence: 99%

Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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“…The conformation of the Di]A structure is not a geometrically continuous double helix but may change locally with the nucleotide sequence. A number of investigations suggested, that structural studies of oliogonucleotides (1)(2)(3)(4)(5)(6)(7)(8) may help to explain conformational effects of nucleotide units in the polymeric state of nucleic acids. In view of several evidences which demonstrated that the conformation of DNA varies with extreme different base composition and local sequence differences (9-14) conformational properties of adenine and thyrine containing deoxyoligonucleotides are of special interest.…”

Section: Introductionmentioning

confidence: 99%

“…ORD and CD results were reported in the series of oligo (dA)'s (6,21,22) and some oligo poly (dA) and poly (dT) in the work of Cassani and Bollum (2). CD differences between cyclic and linear oligo (dT)'s of low chain length reflect large variations in torsional ang,les (5).…”

Section: Introductionmentioning

confidence: 99%

CD studies on the conformation of some deoxyoligonucleotides containing adenine and thymine residues

Zimmer¹,

Birch-Hirschfeld²,

Weiß³

1974

Nucl Acids Res

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CD studies of the deoxyoligomer series d(pT)(n) and d(pA)(n) show increasing CD maxima for oligo (dT)'s with chain length variation from two to seven, while oligo (dA)'s exhibit a decreasing CD maximum. Concentrated solutions of NaClO(4) cause a decrease in the CD of longer oligo (dT)'s towards the CD of d(pT)(2) which is different from oligo dA's. Probably base-sugar interactions are important in the observed conformational effects. The chemically synthesized oligomers dpApApTpT and dpTpApTpA show deviations in their CD spectra which reflect a dominating conformational effect of d(pA)(2) in the former but not in the alternating isomer.

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“…When the sample is cooled to room temperature, this spectrum still appears for several hours then the spectrum corresponding to the associated species slowly appears. This unassociated spectrum is very different from that of the analogous adenine [21] and thymidine [22] derivatives. For both A and T linear dimers, the CD spectrum is in fact similar to that of DNA with positive exciton couplet (positive band at c. 270 nm and negative band at c. 245 nm).…”

Section: Circular Dichroismmentioning

confidence: 64%

Chromonic lyomesophases formed by the self-assembly of the cyclic dinucleotide d(cGpGp)

Bonazzi

Morais

Garbesi³

et al. 1991

Liquid Crystals

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The cyclic dinucleotide d(cGpGp) undergoes a self-association process in water to give, first, columnar aggregates similar to the four-stranded helix of poly(G). Successively, at higher concentration, these aggregates self-organize to give a cholesteric and a hexagonal mesophase, the former of which appears only in biphasic systems. The self-assembly process in isotropic solution has been studied by CD spectroscopy and the structure of the mesophases was investigated by optical microscopy and X-ray diffraction.

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Oligonucleotide interactions. II. Differences in base stacking in linear and cyclic deoxythymidine oligonucleotides

Cited by 25 publications

References 27 publications

Circular Nucleic Acids: Discovery, Functions and Applications

Circular Nucleic Acids: Discovery, Functions and Applications

CD studies on the conformation of some deoxyoligonucleotides containing adenine and thymine residues

Chromonic lyomesophases formed by the self-assembly of the cyclic dinucleotide d(cGpGp)

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