Intercalator–DNA interactions revealed by NIR surface-enhanced Raman spectroscopy

Miljanić, Snežana; Dijanošić, Adriana; Matošević, Igor; Piantanida, Ivo

doi:10.1016/j.vibspec.2011.04.005

Cited by 6 publications

(13 citation statements)

References 34 publications

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“…Since PHENPOD contains phenanthroline, large aromatic surface resembling closely to the phenanthridinium moiety known for its ability to intercalate into ds‐DNA/RNA, intercalation of PHENPOD was investigated in more detail. In our previous SERS studies on DNA/RNA‐intercalating molecules, SERS spectra of their complexes with ct‐DNA were not characterized by appearance of new bands, but by decrease in intensity of the interacalator bands as a result of insertion of the aromatic part of the molecule between the base pairs. To eliminate instrumental factors, such as laser power drift and detector conditions, which affect the band intensity, an intensity ratio of a PHENPOD band and a referent band was calculated.…”

Section: Resultsmentioning

confidence: 94%

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Dijanošić

Miljanić

Piantanida

et al. 2014

J Raman Spectroscopy

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Surface‐enhanced Raman scattering spectroscopy (SERS) in the near‐infrared region had been applied to study interactions of polyaza pyridinophanes with single stranded RNA and double stranded DNA and RNA polynucleotides. Studied compounds, PYPOD and PHENPOD, differed in the central aromatic moiety, pyridine and phenanthroline, respectively, which linked two cyclic amines. An intense scattering was obtained from molecules adsorbed onto the silver nanoparticles, showing nonlinear concentration dependence in the 6.5 × 10−8−6.5 × 10−5 M range. New bands in spectra of PYPOD/polynucleotide and PHENPOD/polynucleotide mixtures were assigned to vibrational modes of polynucleotide moieties involved in interactions. SERS spectra of both polyaza pyridinophanes with single stranded RNA polynucleotides indicated hydrogen bonding between the small molecules and the nucleic bases of poly A, poly C and poly U, whereas an interaction of only PYPOD with poly G was suggested. SERS spectra implied that both compounds bound into the minor groove of the helical poly dAdT–poly dAdT polynucleotide, while none of polyaza pyridinophanes interacted with the grooves of the poly dGdC–poly dGdC polynucleotide. Nevertheless, intensity ratios suggested intercalation of the phenanthroline moiety of the PHENPOD molecules into the double helix of the guanine‐cytosine polynucleotide. Spectral features also indicated binding of the PYPOD molecules within the major groove of the double stranded RNA analog. Copyright © 2014 John Wiley & Sons, Ltd.

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Section: Resultsmentioning

confidence: 94%

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Dijanošić

Miljanić

Piantanida

et al. 2014

J Raman Spectroscopy

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“…15 However, if compared to the Raman spectrum of the crystalline substance, instead of the medium bands at 1651 and 1624 cm −1 , assigned to the CC/CN stretching modes of pyridinium and diimine, respectively, only one band appears at 1637 cm −1 in the SERS spectra of DBTAAbpp (Table 1). In addition, in the SERS spectra a very strong band is obtained at 157 cm −1 with a shoulder at 225 cm −1 .…”

Section: 1mentioning

confidence: 99%

“…Low SERS intensity here implies intercalation of the small molecules within the poly dGdC-poly dGdC helix. 11,14,15 Due to a deep insertion of the planar DBTAA core of DBTAAbpp between the base pairs the molecules are placed away from the silver surface, resulting in a weaker enhancement of the scattered radiation.…”

Section: 31mentioning

confidence: 99%

“…Weak enhancement of the surface scattering obtained from the complexes with the excess of the polynucleotide binding sites points to intercalation as the dominant binding mode. 11,15 It is interesting to note that in the spectrum of the DBTAAbpp/poly rA-poly rU 1/5 complex the intensity ratio of the bands at 1287 and 1267 cm −1 , attributed to the vibrational modes of pyridinium, diimine and phenylene, is 0.95 and is very similar to the value calculated for the free molecules (0.96), at variance to the value of 0.89 characteristic of the DBTAAbpp/poly dAdT-poly dAdT 1/5 complex. Since minor groove binding is proposed as the binding mode with the adenine-thymine polynucleotide and not obtained with the RNA polynucleotide, the calculated ratio could be indicative of interactions of the DBTAA derivative within the minor groove.…”

Section: Interactions Of Dbtaabpp With Poly Ra-poly Rumentioning

confidence: 99%

“…Hence band intensities differ for the free small molecules and those complexed with the nucleic acid, implying changes in position and accessibility of the molecules to the metal upon binding. 11,14,15,20 Here, we report on a detailed SERS study of the binding modes of the DBTAA derivative, DBTAAbpp, with synthetic DNA and RNA (Scheme 1). In order to investigate influence of nucleic base sequence on the binding, double-stranded (ds) polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC and poly rApoly rU) have been used for preparation of the complexes of various DBTAAbpp/ds-polynucleotide ratios.…”

Section: Introductionmentioning

confidence: 99%

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Surface-enhanced Raman Scattering Study of the Binding Modes of a Dibenzotetraaza[14]annulene Derivative with DNA/RNA Polynucleotides

Miljanić¹,

Dijanošić²,

Kalac³

et al. 2012

Croat. Chem. Acta

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Abstract. Binding modes of a dibenzotetraaza14annulene (DBTAA) derivative with synthetic nucleic acids were studied using surface-enhanced Raman spectroscopy (SERS). Changes in SERS intensity and appearance of new bands in spectra were attributed to different complexes formed between the DBTAA molecules and DNA/RNA polynucleotides. A decrease in intensity pointed to intercalation as the dominant binding mode of the annulene derivative with poly dGdC-poly dGdC and poly rA-poly rU, whereas new bands in the spectra at 735 cm −1 and 1345 cm −1 revealed binding within the minor groove of poly dAdT-poly dAdT. When all the dominant binding sites were occupied, SERS spectra implied that small molecules bind on the outside of the DNA analogues, while exist mainly as free molecules in equimolar ratio with the synthetic RNA polynucleotide, thereby indicating higher affinity for DNA than for RNA.(doi: 10.5562/cca2106)

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Hoechst 33258 aggregation and binding to DNA studied by surface‐enhanced Raman spectroscopy

Kenđel

Zavidić

Miljanić

2022

J Raman Spectroscopy

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Interactions of Hoechst 33258 (H33258) with two synthetic DNA polynucleotides, poly dA-poly dT and poly dG-poly dC, as well as natural calf thymus (ct) DNA were studied using surface-enhanced Raman spectroscopy (SERS). Given variety of stoichiometry dependent interactions, complexes were prepared in [H33258]/[DNA] molar ratios of 1/1, 1/5, and 1/10 in the silver colloidal suspension. Prior to analysis of binding modes with DNA polynucleotides, aggregation tendency of the dye in the silver colloid was studied in the concentration range 1 Â 10 À6 -1 Â 10 À4 mol/L. The SERS spectra distinctive of aggregated and monomeric H33258 species were obtained, additionally indicating the form of the molecules bound to DNA. The obtained SERS spectra of H33258 with homo-polymeric polynucleotides implied a deep insertion of the molecules into the AT minor groove, and a partial intercalation between the GC base pairs achieved by the access through the GC major groove. Spectral characteristics of the dye dominated in the spectra of the complexes with ct-DNA, most likely due to random AT and GC sequences of the long natural nucleic acid, affecting uniform binding of the dye and consequently the adsorption of the H33258/DNA complex onto the enhancing metallic surface.

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Intercalator–DNA interactions revealed by NIR surface-enhanced Raman spectroscopy

Cited by 6 publications

References 34 publications

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Surface-enhanced Raman Scattering Study of the Binding Modes of a Dibenzotetraaza[14]annulene Derivative with DNA/RNA Polynucleotides

Hoechst 33258 aggregation and binding to DNA studied by surface‐enhanced Raman spectroscopy

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