Triple helix formation by .alpha.-oligodeoxynucleotides: A vibrational spectroscopy and molecular modeling study

Liquier, J.; Letellier, R.; Dagneaux, C; Ouali, Mohammed Assam; Morvan, François; Raynier, B.; Imbach, J.‐L.; Taillandier, E.

doi:10.1021/bi00091a008

Cited by 29 publications

(26 citation statements)

References 55 publications

(34 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the samples where a reasonable narrow K 3 error range was obtained, the Ai , Ui and Ti fractional concentrations calculated according to Eqn. (9) were used in Eqn. (5) and the corresponding elements of the C matrix were determined by a least-squares fit.…”

Section: Raman and Uv Absorption Spectra Of The Triplex-like Complexesmentioning

confidence: 99%

“…7 The influence of non-natural alpha anomers in purinerich and pyrimidine-rich oligos on triple-helix formation and stability has been monitored by gel retardation and UV spectroscopy 8 and also by vibrational spectroscopy (Raman and FTIR) and molecular modelling. 9 In another study on the role of the sugar moieties in DNA and RNA-DNA triple-helices, it has been shown by means of FTIR spectroscopy that the most stable triple helix is obtained when the third strand contains the 2 0 -Omethylated ribose rings. 10 In other work, the modification of the oligonucleotide backbone was found to increase the stability of triplehelical complexes.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate

Hanuš

Chmelová

Štěpánek

et al. 1999

J. Raman Spectrosc.

View full text Add to dashboard Cite

The formation of poly(rU) complexes with diadenosine monophosphate (3 -5 ) and its four isopolar, nonisosteric phosphonate analogues was studied by means of Raman spectroscopic titration. A set of mixed samples containing the diadenosine monophosphate or monophosphonate and the poly(rU) at various concentration ratios was prepared. The room temperature spectra of mixed solutions were treated by factor analysis and decomposition of the Raman marker bands. For all the species studied, the results revealed an exclusive presence of the triplex-like complexes, i.e. complexes with a 1 : 2 stoichiometric ratio of the adenosine to uridine units, the Raman spectra of which exhibit all the features typical of the poly(rU)·poly(rA)·poly(rU) triple-helical structure. The individual molar fractions of the free ApA dimer, the free poly(rU) and the triplex-like complex do not fit classical equilibrium equation, because the binding ability of the adenosine dimers to poly(rU) falls significantly for small ApA molar fractions. This tendency is strongest for the natural diadenosine phosphate (3 -5 ) and weakest for two analogues in which the -CH 2 -group in the modified internucleotide linkage is situated closer to the 5 -position.

show abstract

Section: Raman and Uv Absorption Spectra Of The Triplex-like Complexesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate

Hanuš

Chmelová

Štěpánek

et al. 1999

J. Raman Spectrosc.

View full text Add to dashboard Cite

show abstract

“…Fourier transform infrared spectroscopy is a technique which allows us to easily characterize the sugar conformations in triple helical structures (31)(32)(33)(34). We have used it to study the sugar conformation in TSC formed in presence or absence of FTIR spectra show that these two structures adopt two different conformations.…”

Section: Introductionmentioning

confidence: 99%

Conformations of Three-Stranded DNA Structures Formed in Presence and in Absence of the RecA Protein

Dagneaux¹,

Porumb²,

Liquier³

et al. 1995

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Using FTIR and UV spectroscopies, we have studied the structures of three-stranded DNA complexes (TSC) having two identical strands, containing all four bases, in parallel orientation. In the first system, an intermolecular TSC is formed by the addition of the third strand (ssDNA) previously coated with RecA protein to an hairpin duplex (dsDNA), in presence of ATP gamma S. In the second one, the formation of an intramolecular triplex is forced by folding back twice on itself an oligonucleotide. The sequences of the three strands are the same in both systems. The formation of the RecA-TSC, which accommodates all four bases, is evidenced by gel retardation assay, and by its biphasic melting profile observed by UV spectroscopy. Using FTIR spectroscopy, N-type sugars are detected in this structure. This shows that in the RecA-TSC studied in presence of the protein, the nucleic acid part adopts an extended form, in agreement with the model proposed by Zhurkin et al. (1,2) and electron microscopy observations (3-6). In contrast, the RecA-free intramolecular triplex in a non extended form has S-type sugars.

show abstract

“…Triple-helical structures involving˛-oligomers as third strands have been shown to form and their geometries were compared with those of the correspondingˇanomers by FTIR spectroscopy. 35 We present in Fig. 4 the Raman spectrum of a triple helix obtained by addition of a third˛-dC 12 strand to poly dGÐpoly dC in acidic conditions.…”

Section: Adc Y 12 ·(Polydg·polydc)mentioning

confidence: 99%

Raman spectroscopy of nucleic acid triple helices

Liquier¹,

Gouyette

Huynh‐Dinh

et al. 1999

J. Raman Spectrosc.

View full text Add to dashboard Cite

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.

show abstract

Triple helix formation by .alpha.-oligodeoxynucleotides: A vibrational spectroscopy and molecular modeling study

Cited by 29 publications

References 55 publications

Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate

Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate

Conformations of Three-Stranded DNA Structures Formed in Presence and in Absence of the RecA Protein

Raman spectroscopy of nucleic acid triple helices

Contact Info

Product

Resources

About