The Structure of Triple Helical Poly(U)·Poly(A)·Poly(U) Studied by Raman Spectroscopy

O’Connor, Timothy; Bina, Minou

doi:10.1080/07391102.1984.10507595

Cited by 16 publications

(3 citation statements)

References 29 publications

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“…Different nucleotide compositions cause the main spectral differences between the DNA complement and the various RNA match or mismatch strands. Differences between the RNA strands are due to variation of only one nucleobase among 9 and therefore they are detectable mainly for intense bands, such as 784 (C, U),20, 21 1230 (U),22 1245 (C),23 1337 (A),24, 25 1481 (G),26 and 1575 cm −1 (A, G) 26. Furthermore, there are also remarkable strong markers of A‐like conformation of sugar–phosphate backbone (810 cm −1 ) 24, 27.…”

Section: Resultsmentioning

confidence: 99%

Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: Model system for evaluation of potential “antisense” drugs

Němeček¹,

Vaisocherová²,

Štěpánek³

et al. 2005

Biopolymers

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Structural features of mismatched base pairs were studied on four nonamer hybrid duplexes formed between the 5'-d(GTGATATGC)-3' complement and its 5'-r(GCAUNUCAC)-3' (N = A, C, G, U) counterparts. This oligonucleotide set is considered a model molecular system for future systematic studies of various modifications of internucleotide linkages with respect to their impact on the structure of mismatched base pairs. Raman spectra, measured at 15 degrees C, revealed the prevailing A-like structure of the RNA strand and mixed A-like and B-like characteristics for the DNA strand. All three mismatches disturb only weakly the overall conformation of the hybrid duplex in contrast to analogous mismatched DNA duplexes. In particular, the dT x rG mismatch influences the global hybrid duplex geometry almost negligibly. The dT x rC and dT x rU mismatches induce somewhat more pronounced distortions of the backbone structure and of the thymine position, the latter being expressed by a change of the surrounding methylene group without effect on the carbonyl's vibrations. Structural effects of the mismatches correlate well with the duplex thermodynamic stabilities obtained by ultraviolet (UV) absorption, i.e., the dT x rG mismatch decreases the hybrid duplex stability very weakly while the effect of both pyrimidine-pyrimidine mismatches is considerable.

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Section: Resultsmentioning

confidence: 99%

Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: Model system for evaluation of potential “antisense” drugs

Němeček¹,

Vaisocherová²,

Štěpánek³

et al. 2005

Biopolymers

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“…Techniques, such as nuclear magnetic resonance (NMR), X-ray fiber diffraction (XRD), and other optical spectroscopies (e.g., circular dichroism, UV-Vis and fluorescence-based methods) have been preferably applied to this purpose [4,6]. To a much lesser extent, structural data on triplex structures have been also collected using Raman spectroscopy [7][8][9][10]. Raman spectroscopy is a vibrational technique which has been lengthily exploited for the detailed structural characterization of biomolecules, including nucleic acid structures.…”

Section: Introductionmentioning

confidence: 99%

Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Guerrini

Alvarez-Puebla

2021

Nanomaterials

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Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

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“…Exhaustive summarizing papers on the topic have been published. 16 -18 In contrast, very little has been discussed concerning Raman studies of triple helices, except for poly rUÐ poly rAÐpoly rU studied in fibers 19 and solution 16,20 and to a lesser extent poly dTÐ poly dAÐpoly dT . 21 We present here recent results obtained in our laboratory by classical multichannel Raman spectroscopy on different nucleic acid triple helices.…”

Section: Introductionmentioning

confidence: 99%

Raman spectroscopy of nucleic acid triple helices

Liquier¹,

Gouyette

Huynh‐Dinh

et al. 1999

J. Raman Spectrosc.

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Raman spectroscopy has been used very successfully to study double-helical structures of nucleic acids and in particular to characterize the geometries of the sugar-phosphate backbone and the base-sugar orientation using Raman lines sensitive to the sugar pucker and the glycosidic torsion angle c (anti or syn). We present here Raman spectra of a series of intermolecular and intramolecular triple helices obtained in solution. A large conformational diversity is found for the sugar-phosphate backbone, which can adopt 'A family' or 'B family' geometries. Depending on the base sequence and the type of sugar (deoxyribose or ribose) present in the strands, characteristic lines around 815 cm −1 [and 836 cm −1 for U·(A·U) triplets] and 840 cm −1 are observed reflecting sugar-phosphate backbone chains with C3 -endo or C2 -endo sugar puckers, respectively. The base-sugar orientation is found to be anti in all triplexes studied. Combination of the Raman data with results obtained by Fourier transform IR spectroscopy and molecular modeling allows third strand base pairing schemes and third strand orientations to be proposed.

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The Structure of Triple Helical Poly(U)·Poly(A)·Poly(U) Studied by Raman Spectroscopy

Cited by 16 publications

References 29 publications

Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: Model system for evaluation of potential “antisense” drugs

Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: Model system for evaluation of potential “antisense” drugs

Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Raman spectroscopy of nucleic acid triple helices

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