J. Liquier

Interpretation of dna vibrational spectra by normal coordinate analysis

1. In the following article we undertake a brief review of the most prominent DNA vibrational markers as observed experimentally by Raman and i.r. spectroscopies on polynucleotides and explain how a simplified valence force field can account for the evolution of the DNA vibrational spectra. 2. Our discussion made as a review of our previous investigations on the interpretation of DNA vibration modes, is based on some of the most characteristic and structure dependent DNA vibrational markers.

Conformational transitions of nucleic acids studied by IR and Raman spectroscopies

Abstract In this short review we first summarize briefly the comparative results obtained in our laboratory by IR and Raman spectroscopies on the right-handed B and the left-handed Z geometries of polynucleotides. The marker IR bands and Raman lines of these conformations are used to present new results concerning the polymorphism of several oligonucleotidic sequences, studied in crystal, solutions and hydrated films by Raman, IR, microRaman and, for the first time, microIR spectroscopies. Finally we give an example of how vibrational spectroscopy can help in the study of interactions between DNAs and drugs. This experimental work has been performed in parallel with a normal coordinate analysis of the DNA marker peaks and this review includes some of the results concerning these calculations and in particular those recently obtained involved with sugar pucker and phosphate backbone markers.

Z Form of Poly d(A-T) · Poly d(A-T) in Solution Studied by CD and UV Spectroscopies

Near UV CD spectra, UV absorption spectra and their first derivatives have been recorded on poly d(A-T).poly d(A-T) solutions in presence of high NaCl concentration and various amounts of NiCl2. Comparison of the results presented here with those obtained for poly d(G-C).poly d(G-C) and poly d(A-C).poly d(G-T) in comparable conditions, and the I.R. and Raman data on poly d(A-T).poly d(A-T), allows us to assign the new spectra to the Z conformation of poly d(A-T).poly d(A-T) in solution. The mechanism by which nickel ions induce the B----Z interconversion in the presence of high NaCl concentration is discussed.

Characterization by FTIR spectroscopy of the oligoribonucleotide duplexes r(A-U)6 and r(A-U)8

Abstract Fourier transform infrared spectroscopy has been used to characterize the helical conformation of double stranded oligoribonucleotides r(A-U)6 and r(A-U)8 in solution. As expected the oligoribonucleotides are found to adopt in solution an A family type conformation. The simultaneous study of a series of duplexes containing A, T or U bases combined either with riboses or deoxyriboses allows us to propose a set of infrared marker bands allowing to distinguish between C2′ endo/anti and C3′ endo/anti conformers of dA, dT, rA and rU nucleosides in nucleic acids.

Triple Helical Polynucleotidic Structures: An FTIR Study Of The C+ · G · C Triplet

Triple helixes containing one homopurine poly dG or poly rG strand and two homopyrimidine poly dC or poly rC strands have been prepared and studied by FTIR spectroscopy in H2O and D2O solutions. The spectra are discussed by comparison with those of the corresponding third strands (auto associated or not) and of double stranded poly dG.poly dC and poly rG.poly rC in the same concentration range and salt conditions. The triplex formation is characterized by the study of the base-base interactions reflected by changes in the spectral domain involving the in-plane double bond vibrations of the bases. Modifications of the initial duplex conformation (A family form for poly rG.poly rC, B family form for poly dG.poly dC) when the triplex is formed have been investigated. Two spectral domains (950-800 and 1450-1350 cm-1) containing absorption bands markers of the N and S type sugar geometries have been extensively studied. The spectra of the triplexes prepared starting with a double helix containing only riboses (poly rC+.poly rG.poly rC and poly dC+.poly rG.poly rC) as well as that of poly rC+.poly dG.poly dC present exclusively markers of the North type geometry of the sugars. On the contrary in the case of the poly dC+.poly dG.poly dC triplex both N and S type sugars are shown to coexist. The FTIR spectra allow us to propose that in this case the sugars of the purine (poly dG) strand adopt the S type geometry.

FTIR Study of Specific Binding Interactions Between DNA Minor Groove Binding Ligands and Polynucleotides

The use of FTIR spectroscopy is made to study the interactions between polynucleotides and two series of minor groove binding compounds. The latter were developed and described previously as part of an ongoing program of rational design of modified ligands based on naturally occurring pyrrole amidine antibiotic netropsin, and varying the structure of bisbenzimidazole chromosomal stain Hoechst 33258. Characteristic IR absorptions due to the vibrations of thymidine and cytosine keto groups in polynucleotides containing AT and GC base pairs respectively are used to monitor their interaction with the added ligands. Although the two thiazole based lexitropsins based on netropsin structure differ in the relative orientation of nitrogen and sulfur atoms with respect to the concave edge of the molecules, they interact exclusively with the thymidine C2 = O carbonyl groups in the minor groove of the alternating AT polymer as evidenced by specific changes in the IR spectra. In the second series of compounds based on Hoechst 33258, the structure obtained by replacing the two benzimidazoles in the parent compound by a combination of pyridoimidazole and benzoxazole, exhibits changes in the carbonyl frequency region of poly dG.poly dC which is attributed to the ligand interaction at the minor groove of GC base pairs. In contrast, Hoechst 33258 itself interacts only with poly dA.poly dT. Weak or no interaction exists between the ligands and any of the polynucleotides at the levels of the phosphate groups or the deoxyribose units.

Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy

Abstract Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K+, Pb2+, Ba2+, Sr2+ and Mn2+ has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2′endo/anti and C2′endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb2+ ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb2+ ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb2+ ions (ΔT = 15 °C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.

Conformations of three-stranded DNA structures formed in presence and in absence of the RecA protein.

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.

Hydration and conformational transitions in DNA, RNA, and mixed DNA-RNA triplexes studied by gravimetry and FTIR spectroscopy.

Abstract We have studied by gravimetric measurements and FTIR spectroscopy the hydration of duplexes and triplexes formed by combinations of dAn, dTn, rAn, and rUn strands. Results obtained on hydrated films show important differences in their hydration and in the structural transitions which can be induced by varying the water content of the samples. The number of water molecules per nucleotide (w/n) measured at high relative humidity (98% R.H.) is found to be 21 for dAn.dTn and 15 for rAn.rUn. Addition of a third rUn strand does not change the number of water molecules per nucleotide: w/n=21 for rUn*dAn.dTn and w/n=15 for rUn*rAn.rUn. On the contrary, the addition of a third dTn strand changes the water content but in a different way, depending whether the duplex is DNA or RNA. Thus, a loss of four water molecules per nucleotide is measured for dTn*dAn.dTn while an increase of two water molecules per nucleotide is observed for dTn*rAn.rUn. The final hydration is the same for both triplexes (w/n=17). The desorption profiles obtained by gravimetry and FTIR spectroscopy are similar for the rAn.rUn duplex and the rUn*rAn.rUn triplex. On the contrary, the desorption profiles of the dAn.dTn duplex and the triplexes formed with it (rUn*dAn.dTn and dTn*dAn.dTn) are different from each other. This is correlated with conformational transitions induced by varying the hydration content of the different structures, as shown by FTIR spectroscopy. Modifications of the phosphate group hydration and of the sugar conformation (S to N type repuckering) induced by decrease of the water content are observed in the case of triplexes formed on the dAn.dTn duplex.

Parallel and antiparallel G*G.C base triplets in pur*pur.pyr triple helices formed with (GA) third strands

Abstract Triple helices with G*G.C and A*A.T base triplets with third GA strands either parallel or antiparallel with respect to the homologous duplex strand have been formed in presence of Na+ or Mg2+ counterions. Antiparallel triplexes are more stable and can be obtained even in presence of only monovalent Na+ counterions. A biphasic melting has been observed, reflecting third strand separation around 20°C followed by the duplex -> coil transition around 63°C. Parallel triplexes are far less stable than the antiparallel ones. Their formation requires divalent ions and is observed at low temperature and in high concentration conditions. Different FTIR signatures of G*G.C triplets in parallel and antiparallel triple helices with GA rich third strands have been obtained allowing the identification of such base triplets in triplexes formed by nucleic acids with heterogenous compositions. Only S-type sugars are found in the antiparallel triplex while some N-type sugar conformation is detected in the parallel triplex.