Biochimie 7ll (1988) 841-846 841 ~) Soci6t6 de Chimie biologique/Elsevier, Paris

Short communication

Particular behavior of the adenine and guanine ring-breathing modes upon the D N A conformational transitions

Mahmoud GHOMI, Richard LETELLIER and Eliane TAILLANDIER

Laboratoire de Spectroscopie Biomol~culaire, U.F.R Biom~dicale de Bobigny, Universit~ Paris-Nord, 74, rue Marcel-Cachin, 93012 Bobigny C~dex, France

(Received 14-10-1987, accepted after revision 3-2-1988)

Summary - - Harmonic dynamics calculations performed on the deoxyguanosine (dG) and deoxyaden- osine (dA) residues, based on a reliable force field, show that the breathing motions of both guanine and adenine residues are involved in two different vibration modes (750-500 cm -I spectral re#on). The calculated results reveal a strong coupling of these modes with the sugar pucker motions. This effect has been verified for the dG residue by the Raman spectra of polyd(G-C). As far as the dA residue is concerned, the particular behavior of the adenine residue breathing mode predicted by these calcul- ations, has been confirmed by Raman spectra of polyd(A-T) undergoing a B--~Z conformational tran- sition.

normal coordinate analysis/DNA/deoxyguanosine-residue/deoxyadenosine-residue/breathing vibration modes

introduction

DNA conformational transitions have been extensively studied by means of vibrational spec- troscopy [1-3]. Among these vibrational modes, the nucleic base breathing motions play a very important role. Strong modulation of the electronic polarizability by these breathing modes gives rise to intense and well-resolved bands in Raman spectra corresponding to oligo- nucleotides and polynucleotides. On the con- trary, these modes are completely non-existent in the infrared spectra because of their negligible effect on the transition dipole moment [3].

In our preliminary calculation [4], it was shown, on the basis of a normal coordinate treat- ment with a Urey-Bradley force field, that the characteristic displacement of the guanine res- idue breathing mode (682---~627 cm -I) arises mainly from the anti ---, syn and the C2'-endo C3'-endo conformational changes relative to the base and sugar in the dG residue upon the B ---, Z transition [5-7].

In this study, we have taken into account the

hydrogen motions and used a valence force field whose harmonic force-constants are derived from our previous work on 5'-dGMP [81 and 2'- dA [9]. The reliability of this force field has been confirmed by the isotopic substitutions and its ability to analyze the nucleosidic motions upon the DNA conformational transitions. In addi- tion to the well-known Raman line-shift men- tioned above, the present calculations show that the guanine ring-breathing motion is also includ- ed in another vibration mode situated around 500 cm -t. This effect had been verified by the Raman spectra of polyd(G-C) and d(C-G)3" d(C-G)3 [1] revealing this mode in both B- and Z-forms. The present calculations predict the same effect for the dA residue, i.e., the appear- ance of the adenine residue breathing motion in two different nucleosidic vibration modes, accompanied by an important shift of one of these modes toward the lower frequencies upon the B --~ Z transition. This calculated prediction was verified by means of Raman spectra derived from the B and Z forms of polyd(A-T) [10].

842 M. Ghomi et al.

Materials and methods

Raman spectra of polyd(G-C) were performed in the original study of Thamann etal. [1]. The positions of the Raman peaks arising from the dG residue in both B- and Z-forms are reported in Table I. Recent- ly, the characteristic Raman lines concerning the dA residue in Z-forms of polyd(A-T): Ni 2÷ were observ- ed [ 10] (Table I). These experimental facts have been used in order to discuss our calculated results.

Harmonic dynamics calculations are based on the Wilson GF-method in which the G-matrix has been calculated using the geometrical data of dG [5-7] and dA [5, 12] found in B and Z helices, respectively. To evaluate the F-matrix, a simplified valence force field has been used and will be discussed in detail in a forthcoming publication.

Computation was carried out on a Cray-ls using a vectorized code which contains a program for the automatic treatment of the redundant internal coor- dinates. To assign the vibration modes the (PED) R matrix elements were used, allowing the correlation of the normal modes to the internal coordinates [ 11].

The theoretical frequencies and the corresponding assignments are given in Table I in the range of 750-500 cm -I. The breathing modes, as visualized on a SECAPA 550-A color-screen, were then drawn on a BBC SE-293 plotter by our graphic programs (Figs. 1 and 2).

Results and Discussion

Both of the vibration modes of the dG residue (B- and Z-forms) in which the guanine residue breathing motion is included are shown in Fig. 1. The first one (Fig. la , b) undergoes a drastic shift to a lower frequency (682 ---> 627 cm-') [1, 2], whereas there is only a very minor change in the second vibration mode around 500 cm -I [1] (Fig. lc, d) upon the B ---> Z transition. Compu- ter graphics clearly show that these base-ring breathing modes are coupled simultaneously to the motion of the sugar puckering. As the poten-

Table !. Guanine and adenine residue characteristic modes.

B-form Z-form

exp. calc. assignments exp. calc. assignments (PED%) (PED%)

dG-re~idue 681 687 C5-C6 (15) 625 637 C3'C2'H NC2N2 (12) CI 'C2 'H N1C606 (7) C2'-C3'

C2-N2 CI'-N9

(21) ~la) (8) (4) (4)

500 498 N1C6C5 (11) 505 504 NIC6C5 (14) CI'-N9 (10) C2N3C4 (10) C4N3C2 (7) C5-N7 (8) C6C5C4 (7) N3-C4 (8) N3-C4 (7) C2-N2 (7)

N1-C6 (6)

dA-residue 727 717 CI 'OI 'C4 ' (13) 716 718 CI'-N9 (11) C3'C4'O1' (11) C1'O1'C4' (10) C4-N3 (1) C2'C1'O1' (8) C6-N6 (1) CI ' -OI ' (8)

C4-N3 (8)

C3'C2'H (10) 622 623 C3'C2'H (27) C2'C3'C4' (11) CI 'C2 'H (22) C3'C2'H (13) C2'-C3' (10)

C2-N2 (4)

666 666

Experimental wave numbers (cm-1) derived from Raman spectra of polyd(G-C) [1]. Kaman spectra af polyd(A-T) [10]. The assignments are based on the internal coordinates.

Behavior of guanine and adenine residue breathing modes 843

GUANOSINE-RESIBUE ZI-FORN (a )

/

1'

EXP. 62ff cm-1 ~R) CALC. 637 cm-1

6UANOSr.NE-RESr.DUE Z r. -FORN

EXP, ffOff cm-1 (R) CALC, ff04 cm-1

(c)

GUANOSINE-RESIDUE B-FORM (b)

EXP. 681 cm-1 (R) CALC. 687 cm-1

GUANOSINE-RESZDUE B-FORN (d)

EXP. 500 cm-1 (R) EALC. 498 cm-q

Fig. 1. Graphic representation of the guanine residue characteristic modes. (a) and (c) calculated with the dG:C3'-endo/syn (Z-form). (b) and (d) calculated with the dG:C2'-endo / arli (B-form). Experimental wave numbers in cm- ] derived from Raman spectra of d(C-G)3-d(C-G)3 Ill. For assignments see Table I.

(a) ADENOSINE-RESIDUE Z-FORM

6 7

• 3 ~ ~

i

EXP. 716 cm-1 (R) GALE, 718 cm-1

ADENOSINE-RESIDUE B-FORM

ADENOSINE-RESIDUE Z-FORM (C)

EXP. 622 cm-1 (R) GALE. 623 cm- I

8"44 M. Ghomi et ai.

EXP. 727 cm-1 (RJ GALE. 717 Gin-1

ADENOSINE-RESIDUE. B-FORM

EXP. 6(;6 cm-1 (R) CALE. 666 cm-1

(b)

(d)

Fig. 2. Graphic representation of thc adenine residue characteristic modes. (a) arid (e) calculated with the dA:C3 ' -endo/syn 1 V (Z-form). (b) and (d) calculated with the dA:C2'-endo / anti (B-form). Experimental wave numbers in cm- deri ed from Raman

spectra of polyd(A-T) [10]. ~'or assignments see Table I.

Behavior o f guanine and adenine residue breathing modes 845

tial energy distribution (PED) a corresponding to these modes shows (Table I), the contribution of the base breathing motion to the higher fre- quency mode in the B-form is more important than in the Z-form, while a completely inverse effect is seen for the mode near 500 cm -~. This effect may explain the change in relative inten- sity of these two characteris'~c modes observed in the Raman spectra of p o l y d ( G - C ) and d ( C - G ) a ' d ( C - G ) 3 [1] showing an intensity ratio variation from 4 to 1 upon the B --> Z conformational transition.

The same kind of effect (Table I) was predict- ed by the present calculations in the dA residues (Fig. 2). The higher frequency mode observed at about 727 cm -1 (Fig. 2a, b) was previously attri- buted to the dA residue in oligomer and polymer Raman spectra [2]. The lower frequency mode, as in the case of dG, undergoes an important shift (666 --> 622 cm -1) upon the B ---> Z trans- ition (Table I, Fig. 2c, d). This striking effect could not be interpreted either by the Raman spectra of p o l y d ( A - C ) . p o l y d ( G - T ) [13] or by those arising from the oligomers containing both A - T and G - C base pairs [2]. In fact, in the B- form, the dA residue vibration mode at 666 cm-! is overlapped (Table I), by the dT residue vibra- tion mode situated at exactly the same frequency [2]. In the Z-form, however, the dA con- tribution is superimposed upon the above-'men- tioned dG characteristic mode around 627 cm -1 [1 9] (Tahla 1, Fig. 1 ~ t3,,r ,'~lcu!ated n,-,~,~i,-- tion was verified by the Raman spectroscopic evidence arising from p o l y d ( A - T ) showing a B --> Z transition in the presence of Ni 2+ ions [10] (Table I).

the base-ring breathing motion can only be observed in P, aman spectra. Moreover, in each case, one of the observed modes situated at 682 cm -l (dG: B-form) and at 666 cm -l (dA: B- form) is shifted to 625 cm -1 when the B --> Z transition occurs. The other mode situated at about 500 cm -1 in the dG residue is less affected by the above mentioned conformational transi- :ion [1]. As p o l y d ( A - T ) goes from the B ---> Z form, the intensity of the dA 727 cm -I compon- ent decreases giving rise to a non-resolved shouldder at about 716 cm -l [10].

The experimental phenomena of the CD signal inversion in p o l y d ( A - T ) [15] simulta- neously with the appearance of a new Raman line at about 625 cm -1 [10] could confirm the abillity of this polynucleotide to adopt the Z- form. Moreover, it has been shown quantitative- ly that by adding the normalized spectra derived from p o l y d ( A - T ) and p o l y d ( G - C ) in the Z- form, one can find the majority of the Raman peaks observed in the Z-form spectrum of p o l y d ( A - C ) . p o l y d ( G - T ) [13]. All these data are in agreement with the calculated results exposed in the present paper.

Due to their breathing characteristics, the modes mentioned above can be used as Raman markers which can be useful in revealing the spe- cific ionic and molecular interaction sites.

More complete calculations on a long-strand polynucleotide or on the oligomers taking into account the base-stacking effect and hydrogen bondings are now advancing on a Cray 2 compu- ter.This attempt allows us to show the effect of the D N A double-helical chain on these nucle- osidic motions.

Conclusion

The similarity in the behaviors of the dG and dA residue breathing modes is the most striking effect revealed by the present calculations. The purine base breathing motion is involved in two observed nucleosidic modes in the 750-500 cm -1 spectral region. Both of these modes are coupled strongly with the sugar vibrations. This fact has also been evidenced in the case of the dG residue adopting the Z conformation in a completely normal coordinate analysis based on d(C-G)3" d ( C - G ) 3 [14]. In fact, because of the very low symmetry of D N A chain components, any vibra- tion mode can be active in Raman and infrared spectra. However , because of the difference in intensity, these characteristic modes involving

Acknowledgment

The authors would like to thank the members of the scientific council of the C.C.V.R. for the calculation facilities.

References

1 Thamann T.J., Lord R.C., Wang A.H.J & Rich A. (1981) Nucleic Acids Res. 10, 5443-5457

2 Benevides J.M., Wang A.H.J., van der Marel G.A., van Boom J.H., Rich A. & Thomas G.J. Jr. (1984) Nucleic Acids Res. 12, 5913-5925

3 Taillandier R., Liquier J. & Taboury J.A. (1985) in: Advances in Infrared and Raman Spectroscopy (Clark R.J.H. & Hester R.E. eds.), vol. 12, Wiley Heiden, New York, pp. 65-113

846 M. Ghomi et al.

4 Ghomi M., Taboury J.A. & Taillandier E. (1984) Biochimie 66, 87-92

5 Dickerson R.E. & Drew H.R.(1981) Proc. Natl. Ac,~d. Sci. USA 78, 7318-7322

6 Arnott S., Chandrasekaran R., Puigjaner L.C., Walker J.K., Hall I.H. & Birdsall D.L. (1983) Nucleic Acids Res. 11, 1457-1474

7 Wang A.H.J., Quigley G.J., Kolpak F.J., van der Marel G., van Boom J.H. & Rich A. (1981) Science 211,171-176

8 Ghomi M. & Taillandier E. (1985) Eur. Biophys. J. 12, 153-162

9 Letellier R., Ghomi M. & Taillandier E. (1987) Eur. Bidphys. J. 14,423-440

10 Ridoux J.P., Liquier J. & Taillandier E. (1988) Biochemistry 27, 3874- 3878

11 Letellier R., Ghomi M. & Taillandier E. (1986) J. Biomol. Struct. Dyn. 3,671-687

12 Wang A.H.J., Hakoshima T., van der Marel G., van Boom J.H. & Rich A. (1984) Cell 37, 321-323

13 Ridoux J.P., Liquier J. & Taillandier E. (1987) Nucleic Acids Res. 15, 5813-5822

14 Vergoten G., Lagant P., Peticolas W.L., Mos- chetto Y., Morize I., Vaney M.C. & Mornon J.P. (1986) J. Mol. Graphics 4, 187-199

15 Bourtayre P., Liquier J., Pizzorni L. & Taillan- dier E. (1987) J. Biomol. Struct. Dyn. 5, 97-104