Influence of uracil defect on DNA structure: 1H NMR invastigation ...

volume 13 Number 9 1985 Nucleic Acids Research

Influence of uradl defect on DNA strncture: 'H NMR Investigation at 500 MHz

A.-M.Delort*, J.M.Neumann+, D.MoIko, M.Herve" + , R.Teoule and S.Tran Dinh+

Laboratoires de Chimie, Departement de Recberche Fondamentale, Centre d'Etudes Nucleaires deGrenoble, 85 X, F.38W1 Grenoble C6dex, and +Service de Biophysique, Departement de Biologic,Centre d'Etudes Nucleaires de Saclay, F.91191 Gif-sur-Yvette C&iex, France

Received 25 Febniaiy 1985; Accepted 22 March 1985

ABSTRACTThe local structure of two self complementary oligonucleotides d(GTAC-

GTAC) and d(GTACGUAC) which differ only by the presence of uracil, not a nor-mal component of DNA,have been investigated by H NMR at 500 MHz. The twooctamers exhibit the same thermodynamical constants (t1/2, AH), their exchan-geable protons broaden and disappear at the same temperature. The T-U substi-tution did not induce any significant changes on non exchangeable protons re-sonances from 2-D COSY and 2-D NOESY experiments. So the two octamers exhibitthe same global structure. The only variation was detected by ID NOE measure-ments : the base orientations around the N glycosidic bonds (x angles) aredifferent.

INTRODUCTION

Uracil is not a normal component of DNA but can occur from different me-

chanisms : i) the incorporation of dUTP residues in place of dTTP by DNA po-

lymerases (1). ii) The in situ deamination of cytosine (2,3). DNA is repaired

by a specific enzyme : uracil-DNA glycosylase which releases uracil by ruptu-

re of the N-glycosylic bond without changing the sugar-phosphate backbone

(3,4,5).

Itecently, using synthetic models, it has been shown that the excision of

uracil is not a random phenomenon. It depends on the position of this base in

the sequence of the oligonucleotide chain (6).

When DNA is double stranded, the conformation of the fragments in the

chain may be of the utmost importance in the efficiency of uracil excision by

uracil-DNA-glycosylase. To investigate the local structure of oligonucleoti-

des containing modified bases such as m'dC (7,8,9,10,11), 2-amino dA (10),

m'dA (12), *H NMR proved to be a very power full tool. These recent findings

prompted us to study the conformation of two self complementary octanucleo-

sides heptaphosphates : d(GpTpApCpGpTpApC) and d(GpTpApCpGpUpApC) which differ

only by the presence of uracil in place of a thymine residue.

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Nucleic Acids Research

MATERIALS AND METHODS

d(GpTpApCpGpTpApC) was prepared in solution by the phosphotriester me-

thod (13). d(GpTpApCpGpUpApC) was synthetized on a solid support by a mixed

phosphotriestet—phosphoramidite method (14,15,16). The oligomers were purified

by reverse phase high performance liquid chromatography using a Nucleosil C18

column with an acetonitrile gradient in 0.1 M triethylammonium acetate (pH

7.0). The procedure was repeated twice. A last purification was performed on a

Sephadex G25 column (PD10 - Pharmacia) with water as eluant. The sequence of

the synthetic octamers were confirmed by the Maxam and Gilbert method (15) mo-

dified by Banaszuk et al. (18).

The pure oligomers were dissolved in 2HjO containing 0.1 M NaCl + 5 mM

POi" and were freed of possible divalent ions by adding EDTA ("V 0.1 mM) . The

pH was adjusted to 7-8 by the addition of a small amount of NaOH. The samples

were lyophilized twice in 2H20 and redissolved in 2H20 to a final concentra-

tion of 2 mM. These solutions were introduced into NMR tubes which were then

degassed in a vacuum line and sealed. 1H-NMR 500 MHz non exchangeable proton

spectra were recorded on a Brulcer WM 500 and referenced relative to internal

3-(tn'methylsilyl)2Hi, propionic acid (TMP) . Proton longitudinal relaxation

rates were investigated using the inversion recovery pulse sequence (180°-

T- 90"- t2).

Two-dimensional J-correlated (COSY) and NOE (NOESY) spectra were recorded

using the pulse sequences (90° - T - ti - 45° - T - t2) and (90° - ti - 90° - T m-

90° - t2) respectively (19-21) with T - 5 us (COSY) and Tm randomly varied by

15 Z around the average value of 400 ms (NOESY). In both experiments : i) a

4-s recycle delay was allowed between each scan and the solvent peak was ir-

radiated during the preparation and evolution periods only, ii) A total of

512 FID's (32 scans), 2 048 data points each was recorded ; after zero-filling

in the ti dimension, a 1 024 x 1 024 data points matrix was obtained and then

Fourier-transformed in both dimensions. Spectra were line-broadened by a sine

bell weigthing in both dimensions.

The exchangeable imino proton spectra in 80 Z 1H20 - 20 Z 2H20 were obtai-

ned by a two pulses sequence (22,23).

RESULTS AND DISCUSSION

I. Exchangeable protons

Figs, la), 1b) show the 500 MHz spectra of exchangeable imino protons of

d(GTACCTAC) and d(GTACGUAC) at different temperatures. In both octamers, below

24° C, two sets of signals with equal areas are observed at 13.7 and 12.7 ppm

3344

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B d - ( G - T A - C - G U A - C )

13.6 13.2 12 .8 ppm 13.6 13.2 12 .8 ppm

Figure 1 - 500 MHz spectra of exchangeable imino protons of d(GTACGTAC) a)and d(GTACGUAC) b) at different temperatures.

d ( G T A C G T A C ) ( A ) , d ( G T A C G U A C ) (B) , 2 2 C

n mr» Mfl n i n

(A)

7.9 7 . 3 6 .3 5 . 7 p p m

Figure 2 - 500 MHz spectra of non exchangeable HI' and base protons of d(GT-ACGTAC) a) and d(GTACGUAC) b) at 22° C.

3345



respectively. In the case of d(GTACGUAC) at 0° C two distinct peaks are obser-

ved for each set, as expected for a self-complementary octamer. In the case of

d(GTACGTAC) the two peaks of the low field region have the same chemical shift.

The low field resonances are assigned to the dA.dT base pairs for d(GTACGTAC)

and to the dA.dT and dA.dU base pairs for d(GTACGUAC) ; the high field resonan-

ces correspond to the dG.dC base pairs (24-28). In both pctawrs, at room tem-

perature, one of the dG.dC base pair signals is broadened beyond detection

and is assigned to the most exposed exchangeable imino protons i.e. those of

the external dG.dC base pair. Above 30° C, with increasing temperature, the

low field resonances (dA.dT base pairs of d(GTACGTAC) and dA.dT, dA.dU base

pairs of d(GTACCTJAC)) broaden and then disappear, followed by the central

dG.dC base pair signal (above 40° C).

These results demonstrate the duplex formation of d(GTACGTAC) andd(GTAC-

GTACGUAC 25*C

3346



B

-1,1

i

A,-3,7

*

6. i

q-a8 1

A

0B

9

<v• V c,-

ur 4

•

6.0 5.6PPH

d

1

5.2

1 2 3 t( G T A C

25

7 A2

G2

6 ' 5 T2

c2

5 6 7GUA*C

'U2«

C2-U2

c8)

Figure 3 - Contour plot of 2-D COSY 500 MHz spectrum of d(GTACGUAC) at 22° C.a) Total spectrum, b) part of spectrum containing the (Hi'-H2>) and (H11-H211)J connectivities.

GUAC). Both duplexes exhibit the same usual opening process with increasing

temperature (24-28).

II. Non exchangeable protons

II.1. Assignment

Figs. 2a), 2b) show the 500 MHz spectra of base and H1' protons of d(GT-

ACGTAC) and d(GTACGUAC) respectively at 22° C. Signal assignment was perfor-

med : i) by comparing at high temperature (t > 80° C) the spectra of the two

octamers ; ii) by recording COSY spectra in order to study the Jn „ scalarIt— a

coupling pattern of each residue ; iii) by investigating the base proton lon-

gitudinal relaxation times (Ti) at high temperature (t > 70° C) and by recor-

ding NOESY spectra at room temperature in order to assign the base proton

resonances. •

For example, fig. 3 shows the contour plot of a 2-D COSY spectrum of d(GT-

ACGUAC) recorded at 25° C (a) and the enlarged region of this spectrum (6)

containing the numerous cross peaks which define the proton (H1'-H2') and

(HI'-H2") connectivities. As far as the bate protons are concerned, at high

temperature, the H6 and H5 signals of the external and internal dC residues

3347



Table I - Longitudinal relaxation time Ti (in second) of d(GTACGTAC) baseprotons at 72° C.

Residue

G1

T2

A3

c"G5

T6A7

c"

H8/H6

2.221.261.761.111.701.231.731.45

H2/H5/CH3

1.18> 72.40

1.09> 73.20

and the H8 signals of the external and internal dG residues can be distinguis-

hed by comparing their longitudinal relaxation times (table I) : the Ti of a

given proton is longer for external than for internal residue (27-29). Final-

d-(G1-T-A-C-G5T-A-C)

2 5 C

M o

o

.3

3

* f *

, • '<

•

7- 00 i. 66

Figure 4 - Part of 2-D NOESY 500 MHz spectrum of d(GTACGTAC) at 22° C contai-ning the intra (H6-CH3) and inter (H6-H8) NOE-connectivities.

3348



TableGUAC)

II - Hj• and base(B) measured at 25

Residue

G1

T2

As

C"

G5

T6

U6

A7

C«

ABA

AB

A

AB

A

ABA

AB

A

AB

ABA

AB

A

Coil

H8/H6

7.8847.895

-0.011

7.4007.3960.004

8.3048.3040.000

7.6187.6040.014

7.8847.895

-0. 111

7.3557.604

8.3288.331

-0.003

7.7997.7960.003

proton chemical shifts of d(GTACGTAC) (A)° C (helix form) and 85° C (coil form).

form (85°

H2/H5/CH3

1.7901.7850.005

8.1438.148

-0.005

5.8745.8640.010

1.7465.737

8.1548.1480.066

5.9565.9490.007

C)

Hi.

6.1676.1490.018

6.0426.049

-0.007

6.3346.3310.003

6.1436.149

-0.006

0.0820.100

-0.018

6.0606.049

6.3836.3810.002

6.2416.246

-0.005

Helb

H./H,

7.9637.9780.017

7.4527.472

-0.020

8.3198.3100.0O9

7.2607.2510.009

7.8277.881

-0.054

7.2387.472

8.2888.310

-0.022

7.3787.3720.006

c form (25

H2/Hs/CHS

1.4304.4140.016

7.6067.5750.031

5.2805.300

-0.020

1.5005.296

7.5467.5107J7O36"

5.3905.396

-0.006

and d(GTAC-

0 C)

Hi-

6.0006.011

-0.011

5.8155.843

-0.028

6.2606.269

-0.009

5.5995.567TT532

5.9305.8430.087

5.7355.843

6.2806.2690.011

6.0806.0720.008

ly fig. 4 shows the region of the 2-D KOESY spectrum of d(GTACGTAC) recorded

at 25° C, containing the cross pecks which connect base protons of either the

same or adjacent residues : connectivities between H6 and CH3 protons of dT

residues as well as cross peaks corresponding to NOE between H8 protons of

dG residues and CH3 protons of adjacent dT residues are observed.

II.2. Helix-coll transition of d(GTACGTAC) and d(GTACGUAC)

Figs. 5a), 5b) show the chemical shift variations versus temperature

(6 - f(t°)) of the base protons of d(GTACGTAC) and d(GTACGUAC) respectively

as well as those of the HI' protons which are well known to be very sensitive

3349



20 40 60 80 100 20 40 60 80 100 T°C

d-(GV-A3-c'-G5-U6-A7-C~)

B

20 40 60 80 100 20 40 60 80 100 T ' C

Figure 5 - Temperature dependence of HI' and base proton chemical shifts ofd(GTACGTAC) a) and d(GTACCTAC) b ) .

3350



Table III - Mid point temperatures (t1/2) and dissociation enthalpies (AH)of d(PTACGTAC) and d(GTACGUAC).

d(GTACGTAC) d(GTACGUAC)

t1/2ext a ) 48° ± 2° c 45° ± 2° C

t1/2. b) 53° ± 2° C 52° ± 2° Clnt

AH c) 40 Kcal/mole A1 Kcal/mole

a) obtained for the external dG and dC residues ; b) obtained for the sixinternal residues ; c) determined from the Log K<j - f(1/T) curves (fig. 6).

to the helix-coil transition (24-28) ; the proton chemical shifts measured at

two extreme temperatures are listed in table II. Inspection of this table re-

veals that at high temperature, the d(GTACGUAC) protons exhibit practically

the same chemical shift as those of the corresponding residues of d(GTACGTAC)

(A6 £ 0.02 ppm). The same phenomenon is observed at low temperature (AS £

0.05 ppm) except for the internal dG5H1' proton (A6 - 0.09 ppm). This compa-

rison is easily evidenced in fig. 2. Moreover, fig. 5 shows that, all the

6 • f(t°) curves (except for the dG!H1' proton) relative to the d(GTACGUAC)

protons coincide with those of the corresponding d(GTACGTAC) protons.

These curves exhibit a sigmoidal form (in the case of significant varia-

tions) characteristic of helix-coil transitions ; the chemical shifts of the

protons in the helix form (low temperature) suggest the presence of a B con-

formation which has been extensively studied by 1H-NMR spectroscopy for va-

rious oligonucleotides during the past few years (24-34). This result is ve-

rified by the following observations : i) the observed NOES between the

guanine H8 protons and the CH3 protons of adjacent thymidines (see above) are

characteristic of a B double helix model where the H8 purine protons are much

closer to the CH3 proton* of the following methylated pyrimidine than to those

of the preceding one (19,35). ii) At 25° C the sums (J1'2'+jr2") (where

J1'2' (J1'2") is the coupling constant between HI1 and H2' (H2")) determined

from the H1' proton triplets (fig. 2) are in the range 14 * 0.5 Hz : this va-

lue is observed when the S conformation (C2' endo) of the sugar ring, charac-

teristic of a B helix, is predominant.

From the <5 - f(t°) curves (with significant variations), the coil and B

helix form proportions (a and 1-a respectively) can be determined according

to the usual relation 6 . - cu5_ + (1-a)<5n where 5_ and 6n are the chemicalODS L H C H

shifts in the coil and B forms respectively. 6- is measured at high tempera-

ture where only the coil form is present and 6_ at room temperature. From

3351



Kd(molt.l-1)

10"

10"

• d (G-T-A-C-G-T-A-C)o d (G-TA-C-G-U-A-C)

2.9 3.0 3.1 1 0 3/ TIKJ

Figure 6 - Semi-log plots of dissociation constant Kj versus reciprocal abso-lute temperature for d(GTACGTAC) (•) and d(GTACGUAC) (o).

these measurements, it is possible to compute the dissociation constant K, -

2a2C/(1-a) where C is the total single strand concentration. Fig. 6 shows the

semi-log plots of K, versus reciprocal absolute temperature for d(GTACGTAC)

and d(GTACGUAC).

The mid point temperatures and dissociation enthalpies of both octamers are

given in table III : the B helix-coil transitions of d(GTACGTAC) and d(GTAC-

GUAC) exhibit practically the same thermodynamic parameters.

Until now, all the results relative to d(GTACGTAC) and d(GTACGUAC) are

similar and no significant effect arising from the U-T substitution was de-

tected. In order to explore more precisely the local conformation of these

two octamers in the B form, the base orientation of each residue of both se-

quences was investigated by determining the NOEs values (in a classical 1-D

steady-state experiment) between the base and sugar protons.

II.3. Base orientations in B helices of d(GTACGTAC) and d(GTACGUAC)

It is now well known that NOE measurements are very useful for studying

the base orientation relative to the sugar (36,37). In particular, let n._,i

and fb_2i (i " 8.6) be the NOEs values observed on the H8 or H6 base protons

upon irradiation of the H1' and H2' sugar protons respectively ; in a first

approximation, the ratio between these two values is given by (36) :

where r^, (r^2?) is the distance between H8 or H6 and H1 ' (H21). This ratio

is directly related to the glycosidic torsion angle X and is very sensitive

to the conformaticmal change around the glycosidic bond because of the r* de-

3352



Table IV - Ratios of NOE values observed on proton He(Ha) upon irradiation ofprotons Hi' and H2 ' (f|6 (e)-2 • /i6(6)-i • ) for the residues of d(GTACGTAC) andd(GTACGDAC) at 25° C.

d(GTACGTAC)

d(GTACGUAC)

Purine

Gi Aj Gi Aj

2.5 3.5 3.5 3.0

6.0 5.5a)b) 5.5a)

Pyrimidine

Ti Cl j! Cf

4.5 5.5 4.5 4.0

2.0 5.0 2.0 6.0

a) H8 signals of dA7 and dA3 collapse; b) H2' and H2" signals of dG5 collapse.

pendence. In fact, terms of relation (1) are average values but we can consi-

der that at room temperature, the hydrogen bonded bases are in a single high-

ly predominant conformation since the helix proportion of the octamers is

practically 100 Z. Table IV lists the R values obtained for each residue of

d(GTACGTAC) and d(GTACGUAC) at 25° C.

As expected, all the values of R are within the range of the anti domain

of the base orientation (in the syn domain, R becomes less than 1) since the

helix structure of both octamers is a B-type. The interesting result is that

the R values obtained for d(GTACGUAC) are significantly different from those

of the corresponding residues of d(GTACGTAC).

In the case of d(GTACGTAC), the values obtained for the purine residues

are close together (R - 3.0 ± 0.5) and lower than those relative to the pyri-

midine residues (R - 4.5 ± 1.0). In the case of d(GTACGUAC), the R values re-

lative to the purine residues are about 1.6 to 2.4 times greater than those of

the corresponding residues of the unsubstituted octamer whereas the R values

obtained for the dT2 and dU6 residues are about twice as low than those of the

corresponding dT2 and dT6 residues. The ratio relative to the dC1* residue is

practically the same in both octamers.

This comparaison shows that i) the most significant variation between the

two octamers involve the dA.dU, dA.dT and external dG.dC base pairs whereas

the internal dG.dC base pairs are unaffected ; ii) if we except the external

dG.dC base pairs because of end chain effects, between d(GTACGTAC) and d(GTAC-

GUAC) the glycosidic torsion x of the two dA residues is increased (with res-

pect to the recent conventions (38)) whereas that of the complementary pyrimi-

dine is decreased (in the usual anti domain, when x+t 1«-2'+ and n«-i'+ then

R+ ; the relative angular variation of x is estimated at 10 to 20°).

These results show that the dU.dT substitution in d(GTACGTAC) duplex

3353



creates a local distorsion of the orientation of the substituted base pair,

which also affects the nearest following base pairs (with respect to the3'-5'

direction) according to the scheme :

5' r*~ 31

G T A C G U A CC A U , G C A T G

31 -*J 5'

CONCLUSION

The study of the spectra at 500 MHz of d(GTACGTAC) and d(GTACGUAC) shows

that the introduction of uracil in place of a thymine residue do not affect

the global structure of DNA : the exchangeable imino protons signals broaden

and disappear at the same temperature, the melting point and dissociation

constants are similar. The assignment of the non exchangeable protons resonan-

ces made by 2D COSY and 2D NOESY did not show any significant effect from the

T-+U substitution. The only variations observed are the modification of the

base orientations around the N-glycosylic bonds (x angles) detectable by 1D-

NOE measurements.

Consequently, it is not a bulky distorsion which is responsible for the

recognition of the uracil defect by the repair enzyme : uracil DNA glycosyla-

se. This result is in agreement with the properties of this enzyme which eli-

minates uracil residues as well in single stranded as in double stranded DNA

chains. In the same way, the enzyme recognizes the changes T •+• U and C ->• U (3,

4,5) though the resulting base pairings exhibit different stabilities.

*To whom correspondence should be addressed

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