5 Number 5 Volume Volume 5 Number 5

1978 May May1978

Nucleic Acids Research Research Nucleic Acids

Theoretical calculations of base-base interactions in nucleic acids: II Stacking interactions in polynucleotides Goutam Gupta and V. Sasisekharan Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, India

Received 1 March 1978 ABS TRACT

Base-base interactions were computed for single- and doublestranded polynucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Pinally, interaction energies of a regular duplex and the alternative structures3 were compared. It was found that the type II model3 is energetically more favourable than the rest.

INTRODUCTION .~~~~~~ In the previous paper we defined two kinds of basestacking patterns normal and inverted types that are observed in single crystals of the constituents of nucleic acids. It is evident that stacking patterns in polynucleotides will be restricted as compared to the stacking patterns that are possible for free bases. This is due to the constraint imposed by the backbone conformation of the polynucleotides. In principle,; both normal and inverted types of stacking should be possible in polynucleotides if the bases can be linked through the backbone without stereochemical problems. We have earlier reported2 that the energy difference between the allowed conformations of the sugar phosphate backbone is rather small and therefore conformational energy of a polynucleotide chain is, to a large extent, likely to be dependent on the base stackin. We have confined our attention first to the nearest neighbour base-base interactions in single C Information Retroval Limited I Falconberg Court London Wl V 5FG England

1655

Nucleic Acids Research stranded polynucleotides; interaction energies for adjacent base sequences in a single chain helical geometry are given. Later, the calculations have been extended to double-stranded polynucleotides. Recently it was shown that both right and left handed double helices are stereochemically possible for polynucleotides3. Hence, interactions between any two adjacent base pairs in right and left handed helical structures have been computed. The interaction energies are, thus given for right stacking (i.e., adJacent bases stacked in a right-helical arrangement) and for left stacking (i.e., adJacent bases stacked in a left-helical arrangement). Interaction energies are also given for inverted stacking arrangements of base-pairs. These have been shown to be stereochemically possible at the bend region of one of the typical alternative3'4 conformations for double-stranded polynucleotides.

METHOD OF CALCUIATION The method of calculation adopted here, is the same as described in the previous paper . The total energy of interaction is thus taken to be the sum of four terms, E =EM +

EMD

+ EW +ERP

.

(1)

where EF, = monopole-monopole interaction,Et = monopoleinduced dipole interaction, ED = London-dispersion energy, and ER= repulsion energy.

The constants and the expressions used in the calculations are the same as given in the previous paper * It may be pointed out that earlier workers5'6 considered bases in a fixed righthelical geometry of B-DNA7. To the best of our knowledge, basebase interaction-energies have not been reported for both right and left-helical arrangements. RESULTS Base-base interactions in a single chains For single-stranded polynucleotides, the calculations essentially refer to basebase interactions in dinucleosides, viz., ApA, GpG, etc., assuming (i) the same geometry and base-orientation designated 1656

Nucleic Acids Research as A geometry, as in B-DNA8 and (ii) the bases in a few examples are perpendicular to the helix-axis, referred to as P geometry. This was done to see the effect of the change in the base-tilt and base-twist on the base-base interactions. The vertical interaction between two bases, for different base sequences, have been grouped as follows% i) homo-dinucleosides (ApA, GpG, CpC, TpT) ii) dinucleosides of complementary bases (GpC, ApT, CpG, TpA) and iii) dinucleosides of non-complementary bases (GpA, TpC, TpG, CpA). Por these cases, the variation of the interaction energy of the two bases, was computed at 50 interval in the helical twist from -50° to +500.

Pig.la shows the energy variation for identical bases in

Figure ls

Variation of interaction energy (Kcal/2 moles of bases) with helical twist e. The bases are taken in the geometry of B-INA as given by Arnott et al., with height per residue, h = 3.4 i.

Figure las

Variation of interaction energy with e for A-A, G-G, T-T and C-C stacking. Solid line for bases in A geometry, broken line for bases in P geometry. 1657

Nucleic Acids Research the A geometry. The most striking feature is that the stacking interaction between C and C (referred to as C-C, this type of representation is used for other bases also) is repulsive for both positive and negative values. The interaction energy is maximum repulsive near 0 = 00 and falls off on both sides of e, and there is no energy minimum. For G-G also, the interaction energy is repulsive and is maximum near 0 = 00. However, there are two shallow energy minima near 0 = +350. The energy minimum at 0 = +350 is lower than the one at 0 -35° by about 2 kcal. On the other hand, the interaction energies for T-T and A-A are attractive for all values of 0. For T-T, there is no minimum and the energy decreases on both sides of ~~~~~~~~~~~~0 a = 00. 0 For A-A, two minima occur at = 5. Thus, minima for A-A and G-G occur near a value of 0 roughly corresponding to the unit twist in B-INA. For A-A and T-T, the energy variation is almost symmetrical whereas for G-G and C-0, the variation is asymmetrical. The difference between the energy values of the corresponding right and left twists is due to the fact that the bases are not exactly perpendicular to the helix axis but tilted by about 60 and twisted by about 20 (Arnott et al.)8. When calculations were performed with bases in the P geometry (bases perpendicular to the helix axis) for identical bases, the energy variation is symmetrical as shown by dotted lines in Fig. la. The different contributions to the base-stacking energy for 0 = +35° are given in Table I. In the case of A-A and T-T, the dominant interaction is ELD which offsets the repulsive interactions due to E. and ERp. In the case of C-C, EMU is dominant and numerically greater than ELD giving rise to repulsive stacking energy, whereas in G-G, the attractive E:D is nearly compensated by the repulsive ESm and ERp giving rise to a small attraction. =

The trend of the results of the present calculations for the right-handed helical twist roughly compares with the results of Pullman and Pullman6, computed for a rightphanded helical geometry given by Langridge et al.7, alithough they did not take into account the repulsive term in their calculations. In parti1658

Nucleic Acids Research cular, they have also shown that the CGC stacking interaction in the B-DKA geometry is repulsive. By turning over the uppe' base, i.e., by keeping it in the syn conformation they have shown that interaction is attractive.

We did not consider the turning a single chain, as such turnovers to syn conformations break the hydrogen bonds of the base pairs. However, interactions between base-pairs in the normal and inverted s tacking arrangements (see earlier paper for the definition) have been computed, results of which are

C-C

over of one base with respect to the other, along

described in

a

later section.

Fig. lb shows the energy variation for dinucleosides of complementary bases such as GpC, ApT, CpG, and TpA (GvCO A.T,

Figure lbs

Variation of interaction energy with 0 for G-C, C-G, A-T, T-A stacking. 1659

Nucleic Acids Research C-G and T-A). The stacking energy in these cases is attractive and the actual value depends on the sequence of the bases, Thus, for T-A the variation of stacking energy with 0 is signifioantly small, and the stacking energy is almost the same for both right and left handed helical twist, and a shallow minimum occurs roughly at 0 = +35 to 45°0 For A-T and G-C, the interaction energy decreases (the rate of decrease varies in the two cases) from 0 = -500 (the numerical value for the energy increases) and reaches a minimum at 0 = 35°0 Thus, A-T and G.C favour right stacking arrangements. The trend of the energy variation for O-G is roughly opposite to that of G-C, and therefore the energy minimum occurs at e = -350 and thus favours a left stacking arrangement. The different contributions to the stacking energy, as before are given in Table I. For this set, as both RI and ELD are negative, the dominant term in the stacking energy is either Eff or BLD depending on the base sequences Calculations for dinucleosides of complementary bases have not been so far reported in the literature for comparison.

Fig. lc shows the energy variation for dinucleosides of non-complementary bases such as GpA, TpC, TpG and CpA (G.!A, T-C, T-G and C-A). Here again, the interaction energy for these examples is negative and the value depends on the base sequence. For T-G and C-A the variation in the energy is relatively small and a shallow minima occur at 0 = + 35 0 How. ever, the variation in energy for T-C and G-A is quite signifi'. cant. The minimum occurs at 0 - -350 for T-C whereas for G'A the minimum occurs at 0 = +350, i.e., T-C favours a left stacking arrangement whereas G-A favours a right stacking arrangement. The energy variation for C-T and A-G (not reported here) will be opposite to the variation for T-C and G-A. Different contributions to the interaction energy in this category are also given in Table I. Again, calculations for these base sequences have not been reported in the literature for comparison.

The above calculations of the dinucleoside bases formed the basis for the interactions between two adjacent base-pairs in a double stranded DNA. We will show in the next section the role of these interaction energies in stabilizing a pair of 1660

Nucleic Acids Research I

u

-o0

I

I

25

s50

I

-2'5 T-G

T- C

E

(kcol /2moles)

-15

Figure les

Variation of interaction T-C, T-G, C-A stacking.

hydrogen bonded base-pairs in

a

energy

with e for G-A,

double stranded DNA.

The interaction between two adjacent base-pairs in a duplexs The dependence of intra- and interchain interactions on the helical twist (Q) was studied in a range of -50° to +500 at an interval of 50. This encompasses both right and left stacking of the bases. Representative graphical variation of the energy with the helical twist (0) is shown for a set of doublets in A and P types. As before the P type was chosen to see the effect of the change in the base tilt and twist on the base-pair interactions. For both the cases the intra- and the interchain contribution to the total interaction energy, are tabulated for a helical twist of 360 and a height per residue of 3.4 as observed for B-INA. Nature of the variation of the interaction energy with the 1661

Nucleic Acids Research Table I

quence Nature Different Contributions To Stacking T ta1 Energy of of Energr (acal/2 moles of bases) E(Kcal/2 mole Bases Helix _E_ of bases) m

Left

A A T T G G C C C

idght Left

RfRigt Lieft Right Left Right Lft G

G C T A A T A G C T A C G

Table Is

EM

EUD

ELD

Enp

+2.2 +1.9 +1.1

-0.4

-10.0

+2.5

-0.5

-10.0 -4.4 -4.4 -10.5

+2.5 +0.6 +0.6 +2.7 +2.7 +0.7 +0.7

+0.5 +7.5 +6.3 +7.8 +5.2 -5.9

-0.2 -0.1

-1.2 -2.2 -1.4 -1.4

-1-.5

Right

-8.3

-0.2

Left

-5. -40

0. -1 .0 | 0.4,

Righit Lueft Right Iniet Right

-

-2,0 1.*2

-10.5 -4.2 -4.2 -2.3 1. -7.

_1.7 -4.9 - _05_ ,-7. 3

-0.1

-5.o4 -3.8

Inert -0.9o

+0.2 -16

Rigt-

-4.1

+0.3

Left

-2._3_

PRih-t

+1.5 +2.3

-1 ,1 +0.0

Left

0.2 -1.8

Right -0.1-, iift + 2.6

0.,7

-0.7+0.7

+0.2

+.5.0 +1.8 +0.1

+0*7 +1.5 +0.8

-5.7 -6.1 -2,9 -3.4 -1.5 -3.3, +2.9 +0.3 -9.5 -6. -11.7 -6.6 -5.8 -7*5 --4.9

+0.4 -4.6 -6.4 tw+1.0 -ne 7 b.9 -13.6 -16.9 .+7.1-6.4-3*4 +0.4 -2.7 --502 +1.00 -3,45 -6.-4 +1.3 -3 .4 +0 . 3 ~ *29 -o7 .1 +1-5 --2.4

Interaction energy of two nearest neighbour bases in a single-stranded polynucleotide in the geometry of B-DNA. The lower base is linked to the upper one through (31-5 ) phosphodiester linkage.

helical twists For a given doublet, the in-plane base-pairing interaction is a constant contribution and does not alter with the helical twist. So in all the graphs, the contributions due to the intra- and the interstrand stacking and the sum of the two are shown. While the interstrand stacking energy is dictated by E and ZM, the intrastrand stacking energy is dominated 1662

Nucleic Acids Research either by or LDor both. The doublets are grouped into two for conveniences (i) in hiich intrastrand stacking is betC A ween purine and purine T A' G C (ii) in which intrastrand stacking is between purine and pyrimidine ' C G C . As we are considering both positive and negative values of the twist, the variation in energy for the remaining T G G are four pairs of doublets, viz. T G TA not given. However, in Table II(a) the energy values for all the pairs are given. Interactions in T A

(graph 2a)s

The interstrand stacking

between T and A is small but attractive, due to negative EBMi The variation of interstrand stacking with helical twist is negligibly small, The intrastrand stacking energy is minimum around 0 350 and so is the total stacking energy. The difference in stacking energy for the two types of base geometry considered in our calculation, is small. For this doublet, both the right stacking and the left stacking arrangements are possible. energy

=

G C

Interaction in

(graph 2b)s

The interstrand stacking between G and C is always attract. tive due to a large negative Ei This stacking energy is minimum for 0 = 0 and numerically decreases on both sides of e. The variation of the intrastrand stacking energy with 0 is just opposite and the contribution of this to the stabilisation energy is small. Thus the doublet is essentially stabilised by interstrand stacking, and the stacking energy minima

occur

around

e

35

=

0

.

The two

minima

are

nearly equal

for

the P type. Whereas for the A type the right stacking arrangement is preferred over the left stacking by about 2 kcal. Interaction in

C

G

(graph 2c)s

The interstrand stacking between A and C, and T and G is always repulsive due to the positive B., and does not change with 0. Whereas the intrastrand stacking energy is attractive throughout and more than compensates the repulsive energy due to the interstrand stacking. The stacking energy minima occur 1663

Nucleic Acids Research at 0 = + 350 and -25 0° The variation in the energy for the two types is not significant. T A (graph 2d)s Interaction in AT The interstrand stacking between T and T, and A and A is always repulsive due to the positive E9. This repulsive energy does not vary with 0. On the other hand, the intrastrand stacking energy is negative for all values of 0. In the oase of A type, the minimum occurs only for a positive value of 3=fO°. For the P type the energy iinima occur at 0 m +25 . Interaction in O G (graph 2e)s

The interstrand stacking between G and G, and C and 0 is repulsive and increases monotonically from 0 (at Q = -50°) to a large positive value (at 0 = +500). Again, this is due to the positive value of E.. The intrastrand stacking energy, on the other hand, increases steadily from -50° to +500. For both A and P types, the right stacking arrangement is favoured over the left stacking. The energy minimum occurs at 0 = +35°. C (graph 2f)s Interaction GT A(gahf) Here the interstrand stacking between T and C, and A and G is attractive due to the negative EMM and does not vary significantly with 0. The intrastrand stacking is also negative and the energy minima occur at 0 = +55 . In the case of P type, the two minima are nearly equal whereas for the A type, the right stacking arrangement is favoured by about 2 kcal. SUMMARY OF THE RESULTS OF INTERACTIONS IN IOUBLETS

In most of the doublets, for the two types of geometry chosen, two minima of the total stacking energy corresponding roughly to 0 = +350 (approximately the unit twist in B-IfiA), are possible, in each type of the base-geometries. The pre" ference of one arrangement over the other is reflected in the energy difference between the two local minima. In general, the depth of the local energy minimaum for a given doublet either in the right or left helical stacking arrangement depends upon three parameters - namely - (i) a tilt of the base with respect to the helix-axis, (ii) a propeller twist and (iii) 1664

Nucleic Acids Research 2(a)

2(b)

1665

Nucleic Acids Research c T

2(c) 5

-

0 A -

-50'

-%P- --43Z

-25'

I(Kcol /2moles) -5

\0~~~~~~~0

-0-

-.0,

0,, m~-6-F-E

-5

2(d) -

1666

'T

A

Nucleic Acids Research 2(e)

2(f) C 1

.-

5

E

CcoI /2moles)

-.0 -250

-5Of

{,, ..s-

_ao--O

4

.~ ~ ~ -C-

A, A~~~~-Ew

%

14

%O\

/0

--

1431~ ~ ~ .0. .,*~

1%

Ckl .

,

d'~0-

-0

0,0

0*

O

.

-15J-

Figure 2: Variation of interaction energy (Kcal/2 moles of base-pairs) with helical twist 0. The solid line corresponds to the variation of interaction energy when bases are in A geometry while broken lines indicate the variation for bases in P geometry. Variation of interaction energy for the doublets: (f) G C (e) C G (d) TA (c) C G (b) GC (a) TA TA

GC

TA

AT

GC

TA

1667

Nucleic Acids Research a displacement of the base-pairs from the helix axis, as defined by Arnott8 et al. It will be noticed that the two types of basew geometry do not alter much the nature of the variation of the interaction energy with the helical twist (curves corresponding to the two types almost run parallel to each other in most of the examples). A systematic analysis of the base-base inter" actions in relation to the three parameters defined above are in progress and will be reported subsequently. Table IIa lists the ten doublet base-pairs in the A type and H[b six doublets in the P type. The corresponding contributions of the intrastrand and interstrand interactions are given. The total interaction for each doublet contains the in-plane interaction including the hydrogen bonds. Our calculations suggest that for A type both right and left stacking arrangements are nearly equally favourable. For the following doubletss G CG T AG OG GO00G AT t2 A T A T A T A' G C while doublets G 'G CO T C favour right helical arrangement, when AT T A G C bases are taken in A geometry. In the case of P type G C favours right stacking whereas O G favours a left stacking arrangement. For all other doublets both right and left stacking are nearly equally favourable. The stabilization energy in the A type is higher than OG doublet C for tGe both for right and left stacking arrangement. In the P type, on the other hand, the energy of C G in the right stacking

AT

GO0

is the same as the energy of aCG the left stacking. This result could have been obtained for the A type also if we had changed the sign of the tilt and twist of the base when compu. ting the energies with negative helical twist. The purpose of the present calculation is to show that both right and left stacking arrangements are possible even with A geometry.

INV RT3D STACKING ARRA.NG BNTS OF BASE-PAIRS The stability of a particular doublet in inverted stacking in a given base-geometry (A or P type) depends upon the contributions from intra- and inter-strand stacking interactions. Thus, the interaction energies of various doublets in both the

1668

Nucleic Acids Research

Iotrastrand

Inter strand Interaction 2norgy(Kcal/4 mol3s of bases Inter In-plane Total inter strand strand Interrgystaciig basapairong action energy energy ols ioteraction of bases) energy

Sequence Nature Intelrof Base of aotion HIelix pairs energy pr H

aln

Table IIaa

I C G

II G C

G C

C G

G G

-19.0 -32.1

+ 3.0 +11.2

Right

-23.3 -13.3

+11.4 + 0.5

C C

Left

+ 1.4

Aighbt

T C

A G

Left Right

3.2 -13.2 -16.2

C T

G A

Left

1 G

A C

Left Right

-

G

C A

Left Right

T A

A T

Left Right

-11.6

T T

A

A

Left Right

A T

T A

Left Right

Left

Rii,ht Left

-

Right

-46.0 -46.0 -46.0

Tot

Total

Interaction energy

(Kcal/4

moles

bases)

-43.0 -34.8

-62.0 -66.9 -57.9

-46.0

-54.6 -45.5

-10.5

-46.0

-56.5

- 8.8

-46.0

-54.8

-55.1 -56. 0

3.5 + 3.4

-31.1

-27.6

-40o.

_31.1

-27.7

-43.9 -42. i

+

-58.6

-14.4 -16.3

+ 2.7

-31.1

+ 3.5

-31.1

-28.4 -27.6

9.1 _11.1

- 4.6 - 3.3

_31.1

-35.7

_31.1

-34.4

-44.8 -45.5

-

5.9

- 3.6

.31.1

-34.7

-40.6

-

8.2

-

9.4

_31.1

_35.5

-43.7

+ 2.2 + 1.6

-16.2 -16.2

-14.0 -14.6

-25.6 -29.5 -26.0 -26.8

_14.9 - 8.8 - 9.5 - 9.5 -

9.8

-

1.0

-16.2

.17.2

-

1.1

-16.2

+ 1.8 + 2.0

.16.2

-17.3 _14.4 -14.2

-10.2

of~

-43.9

-23.9 -24.0

Interaction energy for ten doublets (two covalently linked nearest neighbour base-pairs) in B-DNA. The base-pairs are taken in A geometry. Table Intrastrand

T'

Inter strand Interaotion

Tatal

"nergy (Kcal/4 moles of bases)

of

Base

pairs

I°ta-

motio-

inter-

Sequence

Nature

Inter action In-planeaoir ofeey Helix Total Inter (Knl ener/ staokind Paining rs 4

strand

soles

energy

bases)

of

interacto

inter-

ato

male

nryo

a

otion

energy I

II

ICG G C

Le't Right

-13.1 -28.1

2.0 +12.9

-46.0

-44. 0

-46.0

-33.1

-57.1 -61.2

9.2

-46.0

-55.2

-55.1

9.2

-46.0

-55.2

-55.1

+

i

G

C

Left

G

C

Right

+

0.1

-

C A

G

left

-

8.7

-

3.7

-31.1

-34.8

-43.1

T

Right

-

8.8

-

3.5

-31.1

-34.2

-43.0

Left Right

-15.2 -14.5

+ 3.2

T

+ 3.0

-31.1 -31.1

-27.9 -28.1

-43.1 -42.6

A A

Left Right

-

1.5 1.5

-16.2 -16.2

-17.7 -17.7

-27.1 -27.1

A

Left Right

+

1.5

-16.2 -16.2

-14.7

-25.9 -26.7

G A T

T T A

Table IIbs

C

T

0.1

-

9.4 9.4

-11.2 -11.9

-

+ 1.4

-14.8

Interaction energy for six doublets in B-DNA. The base-pairs are taken in P geometry. 1669

Nucleic Acids Research A and P

types of geometries were computed for doublets in the bend region of type II model. The results are given in Table IIc only for P type of geometry since trend of results are almost the same for A and P type base-geometries. Prom the Tables II it is seen that inverted staocking for a given doublet is enerf'able IIc

Intexstrand

Intrastrand

Interaction

snargy (4cal/4 aioles of bases) Sequenoa interaction of Base energy Lotal intex Intar- In-plana strand Inter(Kcal/4 moles strand base_ pairs action energy of bases) stacking pairing energy

I

II

C

G

G

C

G

c

C A

G T

G

C

Ai

A

A

T

Table IIes

energy

Inter-

action

(Kcal/4 moles of bases)

-13.4

.46.0

-59.4

-61.2

9.5

-46.0

-36.5

-58.6

+ 1.4

_31.1

-29.7

-43.6

- 2.1

_31.1

-33.2

-42.2

-14.0

+ 1.0

-16.2

-15.2

-29.2

-11.6

+ 0.1

-16.2

-16.1

-27.7

_ 1.8

-

22.1

-13.9

~9.0 A~~ T T

'T

interaction

Total

+

Interaction energies for inverted stacking for six doublets in B-IA. The upper base-pair is inverted with reference to the lower one. The base-pairs are taken in P geometry. * In all the tables IIa, IIb, and

IIc, strand I

denotes (3t-51) linkage from lower to the upper base while strand II denotes (31-51) linkage from the upper to the lower base of the doublet. 1670

Nucleic Acids Research getically as favourable as that of right and left stacking arrangements. For examplet stabilization energy (61.2 kcal/ 2 moles of base-pair) for inverted stacking in ¢aGis same as that in right stacking but higher than that in left stacking C (57.1 kcal/2 moles of base-pair). On the other hand, for GG C' inverted stacking has higher stabilization energy (58. 6 kcal/ 2moles of base pair) than the doublet in right or left stacking (55.1 kcal/2 moles of base-pair). Similarly for other doublets, the stabilization energy in inverted stacking compares with right or left stacking, Whichever is higher (e.g., A T A T etc.) or else is higher than the stabilizing energy for both (e.g., A G , G C etc.). Thus inverted stacking is also possible in B-DNA whence Watson-Crick base-pairing scheme is maintained, and allowed stereochemical criteria of the backbone is fulfilled.

COMPARISON OF THE ENERGETICS OF BASE-BASE INTERACTIONS IN THE DOUBIi-HELIX AND THE ATERNATIVE STRUCTURES In a regular duplex, ten doublets give the complete description of base-base interaction. In the alternative models, (both type I and type IIY) continuity of a regular duplex is lost at the bend regions where helical segments of opposite senses are Joined. Therefore, for the base-pair at the bend region, stacking arrangement of the base-pair above is different from that of the base-pair below. Hence, in order to be able to compare the energetics of base-base interaction in the case of double-helix7 9 and the alternative models, energetics of the triplet will gi-ve the correct picture.

Here, for simplicity we will take the triplet in the PPor discussions, four triplets are chosen as representative ones. In the regular helical segments, the energetics will be the same as the double-helix of DNA (as seen from the Table III). The difference will only come at the bend where the continuity of a regular helix is broken. For all the four triplets at the bend region we find, type II model is energetically more favourable than the type I model (or even a regular

geometry.

1671

Nucleic Acids Research Table III

;snergy of- Intexaction (Kcal/ Nature of Rtacking SequeLce Uppex pairs in Bottom Doublet Triplet DoublR t

ilet9)Toa NaturyleI o65.0 oed,f strand interactionenryD Type

of GB igtsefeTp I No Left Left No Right Right I II Type I Right Left Type I Right Left C G G C Right Type II Left Type II Left Right

I

II

T A

A T

I

G

A C

G

a

Left Right Left Right Left Right

Left Right Right Left Right Left

Left Right

Left Right Right Left Right Left

Left

Right Left Right

I I IT A A

l'

Table IIIs

Left

Left

Right Left

Right Right

Right

Left

Right

Left

and typeRight

Intere6.i9. -56.2-

In43.2n

T99.4 -95.45 -95.5

-56.2

-54.1 -54.1 _65.0 -43.2

-142.9

_2.4

-95.3

-29.9

-69.5

-9464

No No

023.1 023.1

-21.3 -21.3

-44.4 -44.4

Type I Type I Type II Type II

-22.4

-21.3

-43.7

023.28 -22.0 -23.5

-21.5

-45.3

No No

Type I Type I Type II Type II

_41.4 -41.4

-262.2

-91.2 -99.4

-22.7

-45.5

_22.8

-46.3

+ 0.2 + O.2 + 0.2

-87.4 -87.4

-87.2

-27.4

-87.2

+0-.2

-7.4

-87.2

-22.0

-68.8

-90.8

-22.0

_68.8

_9048

-87.2

n d r 18.e8 o27.h3l46.1 No

Type I

_1&. 8

_27. 3

_18.6

27. 3

t18. 8

T ype I & 4 II Type 2s. Type II _23. 4

r27.e3 _24.8 _24. 8

-46 .1

t46.1 -46 .1 _48.2 _48. 2

I[nteraction energies f or a f ew double-helical triple t sequence s in regular double-he lice s (left and right ), in the bend region of type I and tyrpe II models.

double-helix of DNA). For all other triplet sequences in P geometry, in the bend region, the type II model is either energetically more favourable than, or equally favourable as type I.

References

1. Goutam Gupta and Basisekharan, V. (1978), Nucl. Acid. Res., previous paper in this issue. 2. Sasisekharan, V. (1973), The Jerusalem Symposium on Quantum Chemis try, 4, 247-260. 1672

Nucleic Acids Research 3. Sasisekharan, V. and Pattabiraman, N. (1976), Curr. Sci., 459 779-781. 4. Sasisekharan, V., Pattabiraman, N. and Goutam Gupta (1977), Curr. Sci., 46, 763-764. 5. De Voe, H. and Tinoco, I. Jr. (1962), J. Mol. Biol., 4, 500-517. 6. Pullman, A. and Pullman, B. (1968), Adv. Quant. Chem., 4, 267-321. 7. Langridge, R., Marvin, A., Seeds, A.W., Wilson, H.R., Hooper, C.W., Wilkins, M.H.F. and Hamilton, L.D. (1960 ), J. Mol. Biol., 2, 38-64. 8. Arnott, S., Dover, S.D. and Wonacott, A.J. (1969), Acta. Cryst., See B25, 2192-2206. 9. Watson, J.D. and Crick, F.H.C. (1953), Nature, 171, 737-738.

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Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides.

5 Number 5 Volume Volume 5 Number 5 1978 May May1978 Nucleic Acids Research Research Nucleic Acids Theoretical calculations of base-base interactio...
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