The conformation of polycytidylic acid, polyguanylic acid, polyinosinic acid, and their helical complexes in aqueous solution from laser Raman scattering

Characterization of low-salt and high-salt conformation of poly(dI-dC) by hydrogen-deuterium exchange kinetics: a classical Raman spectroscopy study

Poly(dI-dC) in H2O and D2O solution can undergo different equilibrium geometries which strongly depend on the salt nature and concentration. These structures were studied by classical Raman spectroscopy in order to monitor a hydrogen-deuterium exchange kinetics in 8-CH group in inosine. Spectral and isotopic exchange rate changes depending on NaCl concentration were observed and interpreted on the basis of previously obtained results from resonance and classical Raman spectroscopy studies of poly(dI-dC) and hydrogen-deuterium exchange measurements of different conformations of nucleic acids. It is shown that: i) the Raman spectrum of low-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for B conformation, but the value of the retardation factor of isotopic exchange suggests that this form is not a pure canonical B form and that it contains some portion of the A form, ii) the Raman spectrum of the high-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for both the A and B conformations, iii) the retardation factor of hydrogen deuterium exchange for the high-salt form of poly(dI-dC) is essentially higher than in the low-salt form which indicates a dominant presence of the A form in the high-salt conformation of poly(dI-dC). This leads to the conclusion that the high-salt conformation of poly(dI-dC) is a mixture of A and B forms with the predominant A form.

A vibrational spectroscopic study of the metastable form of associated polyinosinic acid

We have studied by Raman and ir spectroscopy the metastable complex formed by the self-association of polyinosinic acid in aqueous solution. The complex is easily prepared by quickly cooling to ca. 0 degrees C a warm solution of the polyribonucleotide to which a small amount of rubidium salt has been added. Upon heating, this metastable form melts cooperatively near 13 degrees C, well below the dissociation temperature of a stable four-stranded complex, which occurs at 47 degrees C in the same conditions. The presence of several components in the stretching-mode region of the carbonyl groups in the vibrational spectra of the metastable complex suggests that it also has a parallel four-stranded structure. The difference in structure between the two forms is believed to be caused by the presence of fewer metal ions in the central channel of the metastable complex, in agreement with conclusions reached in previous investigations. The Raman spectra further show that the ribose units in the metastable form have a C3'-endo conformation, in contrast with the stable form, for which we have previously suggested a mixed C2'-endo/C3'-endo conformation.

A vibrational spectroscopic study of the self-association of polyinosinic acid and polyguanylic acid in aqueous solution

We have studied by Raman and ir spectroscopy the structure of self-associated polyinosinic acid and polyguanylic acid in aqueous solution. The results are consistent with the formation of a four-stranded complex, which melts cooperatively near 60 degrees C in the case of poly(I) in the presence of K+ ions. The conformation of the ribose in both systems is mixed C2'-endo/C3'-endo, giving a structure that is intermediate between the extremes proposed previously from x-ray diffraction studies. Characteristic Raman bands for the C2'-endo ribose conformation in polyribonucleotides are identified. The four-stranded structure of poly(I) appears to be very flexible, with approximately 15% of the tetrameric segments being disrupted and approximately 30% of the ribose units adopting a disordered conformation prior to melting. This disordering process increases to approximately 75% above the melting transition, with the remaining approximately 25% of the ribose units keeping an ordered C2'-endo or C3'-endo conformation.

Triple helical polynucleotidic structures: an FTIR study of the C+ .G. Ctriplet

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.

A temperature-dependent Z to B to single-strand transition in d(CGCG)

A thermally induced left- to right-handed helical interconversion for the self-complementary tetradeoxynucleotide d(CGCG) has been observed in the presence of NaCl at concentrations from 1.5 to 2.25M. Analysis of the Raman spectrum of d(CGCG) in aqueous solution as a function of temperature indicates that at low temperature a left-handed Z-helical form is the predominant species. An increase in temperature results in a decrease in the population of the left-handed form and an increase in the population of the right-handed form. Further elevation in temperature results in extensive disruption of base stacking and a loss of secondary structure. This unstacking presumably represents dissociation to a single-stranded structure. The data suggest that a temperature-dependent Z to B to single-strand transition occurs under the conditions employed. A direct Z to single-strand conversion was not identified. In contrast to previous examples, the thermally induced left- to right-handed helical conversion for d(CGCG) can occur in the absence of chemically modified nucleic acid bases, alcohol solutions, or divalent ions.

A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions

The coexistence of both A form and B form tracts and formation of an A-B junction in the oligomer d(GGGGGTTTTT).d(AAAAACCCCC) in saturated sodium chloride solution have been detected by Raman spectroscopy. The entire duplex adopts the familiar B-form conformation in aqueous solution at low salt concentrations (0.1M NaCl). In 6M NaCl the adoption of an A form is observed within the G,C tract while a B-form is maintained in the A.T tract. The experimental results indicate that two different helical forms can co-exist in a rather short oligonucleotide and that formation of an A-B junction can occur over a fairly small span of bases. This is in agreement with recent rules governing the relation between base sequence and secondary structure of DNA published from this laboratory. The conformational preferences of each of the individual oligomers d(AAAAACCCCC) and d(GGGGGTTTTT) have also been investigated. The oligomer d(AAAAACCCCC) is single stranded but some evidence for base stacking is observed at 2 degrees C. In contrast, a double stranded B-form structure characterized by wobble G-T base pairing is observed for d(GGGGGTTTTT) in 0.1M and 6M NaCl.

The structure of triple helical poly(U).poly(A).poly(U) studied by Raman spectroscopy

Using Raman spectroscopy, we examined the ribose-phosphate backbone conformation, the hydrogen bonding interactions, and the stacking of the bases of the poly(U).poly(A).poly(U) triple helix. We compared the Raman spectra of poly(U).poly(A).poly(U) in H2O and D2O with those obtained for single-stranded poly(A) and poly(U) and for double-stranded poly(A).poly(U). The presence of a Raman band at 863 cm-1 indicated that the backbone conformations of the two poly(U) chains are different in the triple helix. The sugar conformation of the poly(U) chain held to the poly(A) by Watson-Crick base pairing is C3' endo; that of the second poly(U) chain may be C2' endo. Raman hypochromism of the bands associated with base vibrations demonstrated that uracil residues stack to the same extent in double helical poly(A).poly(U) and in the triple-stranded structure. An increase in the Raman hypochromism of the bands associated with adenine bases indicated that the stacking of adenine residues is greater in the triple helix than in the double helical form. Our data further suggest that the environment of the carbonyls of the uracil residues is different for the different strands.

Sequence dependence of conformations of self-complementary duplex tetradeoxynucleotides containing cytosine and guanine

The four self-complementary tetradeoxynucleotides which contain only cytosine and guanine are 5'-d-(CpGpCpG)-3', 5'-d(CpCpGpG)-3', 5'-d(GpCpGpC)-3', and 5'-d(GpGpCpC)-3'. The Raman spectra of aqueous solutions (about 0.05 M in monomer) of these tetranucleotides at pH 7 and 2 degrees C show clearly that these self-complementary tetranucleotides form double-stranded duplex structures of the canonical B type when the NaCl concentration is 0.5 M NaCl. If the temperature is raised to 50 degrees C, the Raman spectra show that in each case the double-helical B form melts in a non-cooperative way to a disordered single-chain form. On the other hand, if the salt concentration is raised to saturation, the Raman spectrum of only one of these four tetranucleotide solutions at 2 degrees C is changed in any substantial way. The Raman spectrum of the tetranucleotide 5'-d(CpGpCpG)-3' at 2.2 degrees C and at 4 M or higher salt concentration strongly resembles that of double-helical Z-form poly(dC-dG) taken under similar conditions. We conclude that the tetramer 5'-d(CpGpCpG)-3' is the only self-complementary double-helical tetranucleotide containing only cytosine and guanine in which the B-Z transition can be induced by increasing the salt concentration. This tetramer has several types of stacking interactions which differ markedly from stacking interactions in the other tetramers and may account for the enhanced stabilization of its Z conformation.

Raman spectral studies of nucleic acids. XVII. Conformational structures of polyinosinic acid

Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) complex (Tm=45 degrees C) yields single-stranded and disordered poly (RI) chains. A disordered structure also occurs for poly (rI) in aqueous solutions of low ionic strength. In oriented films, poly (rI) forms an ordered structure probably the same as that which occurs in solutions of high ionic strength. Raman intensities measured at 815 and 1100 cm-1 in spectra of poly (rI) and poly (rU)-poly (rA)-poly(rU) indicate that the correlation previously established for single- and double-stranded ribopolymer structures is valid also for these multi-stranded structures. X-ray diffraction and model-building studies confirm the A-helix structure.

Laser applications in medicine and biology: a bibliography

This bibliography covers the period from 1963 through 1974; 916 references are classified under 23 subject headings. The references are arranged chronologically.

Raman pH profiles for nucleic acid constituents I. Cytidine and uridine ribonucleosides

Raman spectra of aqueous solutions of uridine and cytidine have been recorded as a function of pH with the band intensities and vibrational frequencies monitored to determine bands which may be considered as diagnostic of the concentration of the various species. Quantitative band intensity measurements indicate that not all pH-sensitive bands can be considered as diagnostic of the pK value for the acid form of the nucleoside, and for the percent species in solution. Although the accuracy of the Raman band intensity method is inherently less than that of the titrimetric or visible-ultraviolet spectrophotometric methods, the pK values and percent species agree well with those obtained from these methods. The utility of the results obtained from the pH profiles for cytidine is discussed in terms of the effect of acidification on the structural and conformational characteristics of polycytidylic acid in solution.

Application of Raman spectroscopy to biological macromolecules

The Raman spectra of biological macromolecules arise from molecular vibrations of either the backbone chains or the side chains. The frequencies of the Raman bands lie in a region between 200 cm-1 and 3000 cm-1. From certain frequencies of the vibrations of the backbone chains one can determine the conformation or secondary structure of a macromolecule. Thus for polypeptides and proteins the frequencies of the Amide I and Amide III vibrations allow one to determine the averge conformation of their backbone chain. In polynucleotides and nucleic acids, the frequency of the phosphate diester stretch of the phosphate furanose chain varies between 814 cm-1 for A conformation and 790 cm-1 for B conformation. Raman spectra of the bases in nucleic acids can be used to determine base stacking and hydrogen bonding interactions. Thus Raman spectroscopy is an important tool for determining the conformation structure of proteins and nucleic acids.