Molecular Modeling of Nucleic Acids - American Chemical Society

Chapter 6

Structure and Stability of DNA Containing Inverted Anomeric Centers and Polarity Reversals Downloaded by UNIV OF CALIFORNIA SAN DIEGO on March 30, 2016 | http://pubs.acs.org Publication Date: November 26, 1997 | doi: 10.1021/bk-1998-0682.ch006

1

2

James M . Aramini , Johan H. van de Sande , and Markus W. Germann

1,3

1

Department of Microbiology and Immunology, Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, PA 19107 Department of Midical Biochemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada 2

The promise of controlling gene expression in a specific and efficient manner has spurred a large research effort into antisense DNA therapy (1). To be effective as an antisense drug an oligonucleotide (ODN) must possess a number of properties including: i) nuclease resistance, ii) stable and specific complex formation with the target mRNA, iii) cellular uptake, and iv) the resulting hybrid duplex should be sensitive to cleavage by RNase H. In order to improve the antisense potential of natural ODNs numerous modifications to the phosphodiester backbone, bases and deoxyribose moieties have been explored (2). Our strategy (3) and that of others (4,5) is to employ a combination of alpha anomeric nucleotides in conjunction with 3'-3' and 5'-5' linkages to generate a new class of antisense therapeutics which contain tracts of α- and β-anomeric DNA with improved properties (Figure 1). The 3'-3' and 5'-5' linkages allow the local inversion of the strand polarity of the α-anomeric tracts, enabling the parallel stranded aanomeric component of the O D N to form Watson-Crick base pairs with the R N A target. Recent studies demonstrated that such an approach can lead to the design of ODNs that permit RNase H to destroy the R N A component of an O D N - R N A heteroduplex, a desired property that is not displayed by hybrids containing exclusively α-anomeric D N A (6,7). A n attractive feature of this design is the possibility of generating ODNs that bind much more strongly to the target R N A than phosphorothioates, due to the enantiomeric purity of α-anomeric nucleotides and the inherent stability of a-ODN/β-ΙΙΝΑ hybrids (8), and are also nuclease resistant and capable of activating and directing RNase H. These properties make oligonucleotides with polarity and anomeric center reversals viable candidates for antisense molecules. In this chapter we give a synopsis of our recent enzymatic, thermodynamic, and spectroscopic investigations of ODNs containing α-anomeric nucleotides and polarity reversals (7,9,10). RNase H Studies Alpha Winged ODN/RNA Duplexes are Susceptible to Cleavage by RNase H . Mixed anomeric sequences with polarity reversals can activate RNase H . For example, we have investigated the RNase H sensitivity of constructs containing short tracts of β-anomeric nucleotides flanked by alternating α/β-anomeric wings (Figure 3

To whom correspondence should be addressed: Tel (215) 503-4581; F A X (215) 923-2117; E-mail: [email protected].

92

© 1998 American Chemical Society

Leontis and SantaLucia; Molecular Modeling of Nucleic Acids ACS Symposium Series; American Chemical Society: Washington, DC, 1997.

Downloaded by UNIV OF CALIFORNIA SAN DIEGO on March 30, 2016 | http://pubs.acs.org Publication Date: November 26, 1997 | doi: 10.1021/bk-1998-0682.ch006

ARAMINI ETAL.

DNA Containing Inverted Anomeric Centers

Figure 1. Schematic diagram of a β-α-β stretch, in which the α-anomeric nucleotide is fused to the flanking β-nucleotides via 3 ' - 3 ' and 5'-5' phosphodiester linkages. The Γ , 3' and 5' furanose ring positions are labeled; Β = nitrogenous base. α-Anomeric nucleotides differ from their natural β-counterparts by a single inversion of stereochemistry at the C I ' position.


94

MOLECULAR MODELING OF NUCLEIC ACIDS


2). The wings are composed of four sets of 3'-3' and 5'-5' linkages, and thus, are thermodynamically not optimal compared to flanking sequences containing purely aanomeric nucleotides due to the large number of junction components. However, these wings convey nuclease resistance and, as intended, direct the action of RNase H (Figure 3). For both dA4 and dT4 we observe highly localized E. coli RNase H mediated R N A cleavage just outside the β-anomeric recognition window, directly across from the 3'-3' linkage, resulting in the production of 8- and 12-mers, respectively. The low temperature (13 °C) digest reveals that the dA4 hybrid is more readily cleaved by the enzyme while at higher temperature (21 °C) both reactions went to completion. α-Containing ODNs Activate RNase Η and Destroy RNA Targets in Substoichiometric Amounts. The ability of alpha winged ODNs to activate RNase Η was studied in more detail. Of particular interest from a biological point of view is whether or not these ODNs can sustain processive cleavage of R N A targets. Our data (Figure 4) show that a substoichiometric amount of the dA4 O D N (10%) results in the near complete digestion (80%) of a 10 fold larger amount of the complementary R N A strand. As the reaction nears completion very little R N A remains, with the consequence that the RNA-ODN duplex becomes progressively less stable; complete degradation was observed at a lower temperature (21°C). This demonstrates that RNase H cleavage of these duplexes is indeed catalytic, with each dA4 O D N being used an average of eight times. Furthermore, we did not detect any evidence for the degradation of the ODN (data not shown). Spectroscopic Studies of α-Containing DNA Duplexes Sequences. In an effort to gain insight into the thermodynamic and underlying structural effects of the introduction of α-anomeric nucleotides and polarity reversals into D N A in a systematic fashion, we have examined a self-complementary decamer model system based on the well-known Dickerson dodecamer (Figure 5). The series consists of an unmodified control, plus four constructs containing a single α-anomeric nucleotide (either aT, aC, a A , or aG) flanked by 3 ' - 3 ' and 5'-5' phosphodiester linkages; the latter serve to reverse the polarity of the α-nucleotide within the predominantly β-anomeric sequence, thereby facilitating base pairing to its complement. As a secondary control, we have also investigated a sequence containing one α-anomeric residue but lacking polarity reversals (alphaT2). Finally, the core of the model sequence corresponds to the EcoKl consensus recognition sequence, which provides an additional built-in means of assaying the structural perturbations resulting from the unnatural moieties; our EcoKl enzymatic studies on this series of constructs are beyond the scope of this summary (10). Thermodynamic Properties. U V thermal denaturation studies of the decamer family demonstrate that the insertion of two parallel stranded α-anomeric nucleotides in a decamer, along with four polarity reversal junctions, results in a relatively small penalty to the thermal stability of the duplex (Table I). On the basis of the T and AH° values, we conclude that duplex stability decreases from the control to alphaC in the following series: control > alphaT « alphaA « alphaG » alphaC. Interestingly, we observed that alphaT is prone to hairpin formation under conditions of low concentration and elevated temperature. This is an inherent property of selfcomplementary D N A duplexes (77), and can be attributed to the modifications in the central portion of the helix, thereby destabilizing the duplex relative to the hairpin form. Such behavior is very dramatically observed for the alphaT2 sequence, in which the incorrect polarity of the α-nucleotide hampers base pair formation and results in the severe destabilization of the duplex form (see Studies of alphaT2 below). m



6. ARAMINI ETAL.

5'


95

r- A G G U d- f y C x ( g y A

U A

U U A ^ A A A U U G G G-3' A AxSyT T Tx&yA Cx(§yC-5'

r- A G G U d- S y C x € y A

U A

U U A A A A U " U G G G~3' Ax^yT Τ T TxâyA Cx(gyC-5'

dA4

5'

dT4

5'

control

3 ' d - T c c A A A A T T T T A A c c

5'

5

'

r

-

A

G

G

U

U

U

U

A

A

A

A

U

U

G

G

G-3

Figure 2. Sequences of the alpha-winged RNase H substrates and their control. In the D N A strand, y indicates a 3 '-Ύ linkage, χ a 5'-5' linkage, and α-anomeric nucleotides are depicted in outline type. In the dT4 and dA4 hybrids, RNase Η sensitive windows are denoted by bars, and the major cleavage sites are marked by arrows.

Figure 3. Denaturing gel electrophoretic analysis of RNase Η digestion products of RNA alpha winged ODN hybrids. C, control; 1, dT4; 2, dA4; M , Markers. The reaction temperature was 21 °C for lanes C, 1, and 2 and 13 °C for lanes l a and 2a. e


7

C-5'



100'

50

100

150

200

250

Time (min) Figure 4. RNase H degradation of the R N A target ( U U U U ) in the presence of substoichiometric amounts of the dA4 O D N at 30° C. The target R N A was present in a 10 fold excess over ODN. R N A was P labeled and quantified by scintillation counting after bands were excised from denaturing gels. The thick line in the plot represents a turnover number of unity. 3 2

|

U

T

O

alpha 12

S ' - G C G A A T c e C G C

c G c a f T A A G C

G-5'

alphaG

5 ' - G C a © A A T T C G C C G C Τ Τ A A a © C G-5'

alphaA

- G C G O & A T T C G C C G C T T A a & G C G-5'

alphaC

-G C

A Τ

C G A G α© τ

Τ A

Τ a© G A G C

alphaT

S ' - G C G A A T a ' â P C C G C ex's? T A A G

control

5'-G C G ^ A A Τ T C G C G C T T A A j ^ G C

.

C G-5'

G C C G-5'

»~

C G-5'

Figure 5. Sequences of the family of self-complementary α-containing decamer duplexes we have investigated and their control. Arrows indicate the strand polarity in the 3'->5' direction; the 3'-3' and 5'-5' phosphodiester linkages are denoted by tail-to-tail and head-to-head junctions, a-Anomeric nucleotides are shown in outline type. Black arrows in the control duplex represent the EcoRl restriction enzyme cleavage sites.


6. ARAMINI ET AL.


97

Table I. Thermodynamic Data for the Control and α-Containing Decamer Duplexes** duplex AS° (kJmoWK- ) AH° (kJmoF) T (°Q ( C = 30uM) control 59.8 (0.1) 343 (12) 0.940 (0.033) alphaT 54.7 (0.3) 330(15) 0.946 (0.021) alphaC 49.8 (0.3) 258 (7) 0.712(0.022) alphaA 54.4 (0.2) 323 (13) 0.898 (0.041) alphaG 54.3 (0.3) 334(14) 0.933 (0.043) A l l measurements were performed under the following buffer conditions: 400 m M NaCl, 10 m M Na.2HPC>4, 0.1 m M EDTA, pH 6.5. Thermodynamic data were obtained from analysis of melting curves using a six parameter fitting routine assuming a two-state (helix coil) transition and accounting for the temperature dependent absorbances of the helix and coil forms, as well as the concentration dependence of the T (10,12). Standard deviations are given in parentheses. (Reprinted from ref. 10. Copyright 1997 American Chemical Society). 1

m

T


a

m

NMR Studies. In the following sub-sections we present the salient N M R spectroscopic results which conclusively demonstrate that the α-containing duplexes are structurally analogous to the control (i.e., anti-parallel, right-handed B-DNA). Overall, our data indicate that structural perturbations in these species are localized to the regions encompassing the α-nucleotide and unnatural phosphodiester linkages, although subtle differences do arise depending on the nature of the α-nucleotide. The N M R data corroborates the results of other spectroscopic techniques, namely circular dichroism and U V hyperchromicity, which are not presented here. 1

l

Imino H NMR. Imino H N M R spectroscopy is a powerful direct probe for the presence and nature of the base pairing in nucleic acids. As shown in Figure 6, the imino K spectra for the control and the four stable α-containing duplexes exhibit resonances for the five chemically distinct imino protons in each self-complementary decamer, indicative of stable base pair formation. In addition, temperature dependent experiments showed no evidence for pre-melting of the base pairs comprising the anucleotides. Virtually identical N M R spectra have been obtained for the α-duplexes at optical concentrations (3 to 6 μΜ duplex), demonstrating that the duplex form exists under the conditions used in the thermodynamic studies. l

NOESY walks. For the assignment of non-labile *H N M R resonances in B D N A it is standard practice to employ two major NOE pathways, specifically the sugar H I ' base H6/H8 and sugar H 2 7 H 2 " base H6/H8 pathways (13). In all of the α-containing decamers we observe that the Η Γ network remains intact, as in the control. However, in each case the H 2 7 H 2 " pathway is broken between the anucleotide and the subsequent residue. This effect is due to a flip in the orientation of deoxyribose ring of the α-nucleotide, which places the H 2 " proton too far away from the base moiety in the following residue to make an NOE contact (Figure 7; also see Models below). Deoxyribose ring conformation. Intraresidue spin-spin (J) coupling patterns are highly diagnostic of the type of sugar puckering adopted by deoxyribose rings (14,15). It is widely believed that the deoxyribose moiety in D N A undergoes a rapid conformational exchange between the so-called N - and S-type puckers, meaning that the observed /-coupling constants for vicinal protons in the ring are a weighted average of the couplings for the two inter-converting forms according to equation 1 : ^XYobs =

N

(1-/S)/ XY+/S^XY


(1)

98


G3*


alphaG

alphaA

alphaC

alphaT G9/G1

T7 6 T

control

14.0

13.5

13.0

12.5

l

ppm

Figure 6. Imino proton region of the U (600.1 MHz) N M R spectra of the control (2.6 mM), alphaT (6.8 mM), alphaC (2.4 mM), alphaA (2.9 mM), and alphaG (2.2 mM) duplexes in 90% H O/10% D 0 , 50 m M NaCl, 10 m M phosphate buffer, pH 6.5, 293 K . Note that the imino proton signals for G l and G9 in the control and alphaC decamers are degenerate under these conditions. In each of the α-containing duplexes the imino proton within the base pair involving the α-nucleotide is denoted by an asterisk. (Reproduced from ref. 10. Copyright 1997 American Chemical Society). 2

2



ARAMINI ET AL.


Figure 7. Schematic diagram showing the Η Γ H6/H8 (thick arrows) and H 2 7 H 2 " H6/H8 pathways in the T-3'-3'-aC-5'-5'-G stretch of the alphaC decamer. Note the break in the H 2 7 H 2 " H6/H8 network between H 2 7 H 2 " of the α-nucleotide and H8 of the guanosine.




100

where/s is the mole fraction of the S-pucker. On the basis of the sum of the Η Γ coupling constants (ΣΓ; Table II) and spectral simulations (16,17), illustrated in Figure 8, we conclude that the /-coupling data for all nucleotides in the control duplex, as well as the vast majority in the four α-containing species, are indicative of a high S-character (i.e., large Σ Γ , Jyr > J\'2~, very small h~y)\ this is the normal situation in B - D N A . However, in three cases (alphaT, alphaC, and alphaA) we find that the conformational equilibrium of the deoxyribose ring in the nucleotide following the 5'-5' phosphodiester linkage is drastically shifted away from a high Scharacter (fs ~ 40 to 60%; see Table II). In light of analogous decreases in fs for deoxyribose groups within D N A / R N A hybrids reported in the literature (18), this effect may have biological ramifications. The sugar moiety in A 4 of the alphaG decamer as well as those in all nucleotides preceding 3'-3' linkages are not perturbed.

Table II. Sugar Puckering Data for the Nucleotides Following the 5'-5' Phosphodiester Linkage in the α-Containing Decamer Duplexes** G9 C8 ΣΓ decamer decamer Σΐ' fs fs control 15.1 15.7 1.00 control 0.90 0.63 alphaT 13.5 12.9 0.53 alphaC A4 A5 decamer ΣΓ ΣΓ decamer fs fs control 15.7 1.00 control 16.2 1.00 0.80 alphaA 12.1 14.5 alphaG 0.39 Data obtained from the Η2"(α>ι)/ΗΓ(ω2) multiplets along ω in resolution enhanced D Q F - C O S Y , P.E. C O S Y , or E . C O S Y spectra. Values of / were calculated using the following expression (14): fs = ( Σ Γ - 9.8)/5.9. (Adapted from ref. 10). a

2

s

3 1

P NMR. Given our use of unusual phosphodiester linkages, the backbone conformation is of crucial importance in our studies of these duplexes. It is wellestablished that the chemical shift of the phosphorus atom is very sensitive to changes in backbone conformation in nucleic acids (19). P N M R spectra of the control and the four α-containing duplexes are shown in Figure 10. With the exception of the large (± 1.1 to 1.5 ppm) chemical shift changes observed for the 3 '-Ύ and 5'-5' phosphodiester linkages, the vast majority of phosphates resonate in a narrow window of the spectrum corresponding to that for the B - D N A control. The major exception to this is the phosphate directly across from the 3'-3' linkage in alphaC (i.e., GpA), which experiences a +0.6 ppm shift compared to the control duplex. Downfield shifts of this magnitude have been repeatedly observed in duplex D N A containing mismatches (20), and are thought to be due to changes in the relative populations of the commonly observed B i backbone conformation and the higher energy Β π form, toward the latter. 3 1

Models. The models of the alphaA and control decamer duplexes shown in Figure 9 are consistent with our spectroscopic data on several grounds. First, the models are in agreement with the finding that the local inversion of the strand polarity at the a A position enables this nucleotide to form a regular Watson-Crick base pair with the Τ residue on the complementary strand, fitting snugly into the helix while maintaining the base stacking. Second, the bases are in the anti orientation, with the exception of aA4. This residue is formally in the syn range; however, the H8-H1' distance is similar to that expected for β-anomeric nucleotides in an anti conformation. Third, the observed Η Γ H6/H8 and H 2 7 H 2 " H6/H8 N O E pathways are consistent Leontis and SantaLucia; Molecular Modeling of Nucleic Acids ACS Symposium Series; American Chemical Society: Washington, DC, 1997.


6. ARAMINI ETAL.


Figure 8. Expansions (60 χ 40 Hz) of six DQF-COSY cross-peaks (white boxes) for the C8 residue in the control and alphaT duplexes (303 K) and their corresponding simulations (blue boxes). Simulations were obtained with the SPHINX and L I N S H A routines (16) using the approach of the James group (17). Negative contours are shown in red; positive contours are black. The following coupling constants produced the best fits: control, Jvr = 9.1, / η - = 5.9, J = 6.2, J = 3.0, J - = -14; alphaT, J = 6.0, J\'2" = 6.5, J y = 6.3, J "y = 5.3, J - ~ = -14. Sugar puckering results based on contour plots of the above couplings plus bounds (Jyr, Jv2"> J l'y ± 0.5 Hz; /2"3' ± 0-5 to 1.0 Hz) as a function of fs and Ps assuming a twostate equilibrium in which P^ = 9° and Φ = Os = 35° (14) are as follows: control,/s = 81 - 93%; P = 145 - 185°; alphaT,/ = 46 - 58%; P = 150 200°. r y

2

r y

2

r2

2

v r

2

ν

s

s

s


101


102


Figure 9. Models of the control (A) and alphaA (B) decamer duplexes. The initial models were based on the PDB coordinates of the Dickerson dodecamer (22), and energy minimized with A M M P , "Another Molecular Modeling Program" (23), as outlined previously (9,10). A dielectric screen with 5 Â correlation length and no cut-off for non-bonded interactions were used; also no N M R (i.e., N O E or J) restraints were incorporated into the calculations, a-Anomeric nucleotides are displayed in red. Both duplex models are nearly identical, with an R M S D of 0.32 Â (excluding the ccanomeric residues and their counterparts in the control), and total energies of -12419 kJmol- for alphaA and -12461 kJmoF for the control. The sugar puckering for each nucleotide in the models shown, including A5 in alphaA, is of the S-type. 1


6. ARAMINI ET AL.


103


with the corresponding distances in the models; specifically, the Η Γ base NOES Y walk can be followed throughout the entire sequence in both duplexes, whereas the H 2 7 H 2 " base NOE pathway is disrupted between ccA4 and A5 in alphaA, because of the increased distance between the H 2 7 H 2 " of the α-nucleotide and the subsequent base. Similar conclusions have been drawn from the modeling and N M R studies of the remaining duplexes in this family. Studies of alphaT2. The spectroscopic and modeling studies discussed above indicate that the linkage reversal (i.e. a local parallel strand disposition at the aanomeric nucleotide) is a prerequisite for stable duplex formation. This is in agreement with the conclusions drawn by other groups based on U V melting studies (4). A recent molecular mechanics study proposed that an α-anomeric nucleotide (aA) would base pair and contribute to the overall duplex stability if it is present in an antiparallel strand orientation, thus obviating the need for the unusual 5'-5' and 3 '-Ύ phosphodiester linkages (24). We have investigated this possibility by studying a sequence analogous to the alphaT decamer (i.e. alphaT2 in Figure 5) which does not contain linkage inversions. The comparison of alphaT and alphaT2 assesses the energetic and structural requirements of the strand disposition of α-anomeric nucleotides on duplex stability. The alphaT2 sequence is characterized by a low melting temperature as well as a shallow melting profile. The melting temperature was found to be independent of the strand concentration at optical strand concentration, consistent with hairpin formation. This was confirmed by imino proton spectra recorded for a 12 μΜ alphaT2 sample at 283 Κ (Figure 11 A). Under these conditions three GC base pairs are observed at δ « 13 ppm as well as the two T-loop imino protons at δ « 11.4 and 10.8 ppm, in agreement with previous studies on D N A hairpin structures with T-loops (25). These results are also consistent with the resonances observed in the methyl group region, where for either pure hairpin or pure duplex forms two methyl group signals are expected. Based on the imino and methyl group signals, a significant amount of hairpin is detected even up to 5.4 m M strand concentration (Figure 1 IB). Increasing the temperature to 303 Κ results in a shifting of the equilibrium to the hairpin form. The low thermodynamic stability and the strong tendency of alphaT2 to form hairpins demonstrate that a parallel strand disposition is indeed a requirement of α-anomeric nucleotides for the formation of stable duplex structures. Conclusions and Future Prospects Antisense ODNs containing a β-anomeric core flanked by nuclease resistant aanomeric segments are capable of eliciting RNase Η activity while retaining strong hybridization to the R N A target sequence. Such an ODN was shown to be able to mediate the degradation of an R N A target in substoichiometric amounts inescapably implying multiple turnover of the ODN. Ultimately any O D N must be eliminated from an organism. It is noted that endonucleolytic cleavage of the β-anomeric core of these ODNs will disable their antisense potential thereby minimizing the probability of nonspecific antisense activity of breakdown products. Our systematic structural and thermodynamic analysis of a D N A decamer model system containing α-anomeric nucleotides has established that the α-anomeric components fit snugly into the double helix causing only local perturbations. In particular, base stacking and specific base pairing was retained for all α-anomeric nucleotides investigated, but only if they were provided with a local parallel stranded environment. However, we observed unique deoxyribose ring and backbone perturbations dependent on the nature and position of the α-nucleotide and polarity reversals in the sequence. We are currently investigating strategies to enhance the stability of the acontaining sequences by alleviating constraints imposed by the unusual phosphodiester linkages. Leontis and SantaLucia; Molecular Modeling of Nucleic Acids ACS Symposium Series; American Chemical Society: Washington, DC, 1997.

104



5'-5'

3'-3'

control

'

1 1

I

1 1

'' I

1.0

1 1 1 1

1

I '

0.5

1 1

I

0.0

1 1 1 1

-0.5

I

1 1 1 1

1 1

I ' 'I

-1.0

1 11

-1.5

ppm

Figure l O . ^ P (242.9 MHz) N M R spectra of the control (2.6 mM), alphaT (6.8 mM), alphaC (5.9 mM), alphaA (5.1 mM), and alphaG (2.2 mM) duplexes in D2O at 303 K. Resonance assignments were made using the H detected P - H correlation technique of Sklenâr et al. (27). (Reproduced from ref. 10. Copyright 1997 American Chemical Society). 1

3 1

1

1

ι

ι 13

ι 12

11

ι ppm

ι—•—ι—•—ι—•—ι—•—ι—•—1—'— 2.0 1.8 1.6 1.4 ppm

Figure 11. Imino proton and methyl group regions of the *H (600.1 MHz) N M R spectra of alphaT2 in 90% H O/10% D 0 , 50 m M NaCl, 10 m M phosphate buffer, pH 6.6, 283 K . A) Strand concentration 12 μΜ; Β) strand concentration 5.4 mM. 2

2


6. ARAMINI ETAL.


105

Acknowledgment This work was funded in part by a grant from the Natural Sciences and Engineering Research Council of Canada (JHvdS). References


1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25.

Wagner, R. W. Nature 1994, 372, 333-335. De Mesmaeker, Α.; Häner, R.; Martin, P.; Moser, H. E. Acc. Chem. Res. 1995, 28, 366-374. van de Sande, J. H.; Kalisch, B. W.; Quong, B. Q.; Germann, M. W. 1994 Antisense Oligonucleotides with Polarity and Anomeric Center Reversals. First International Antisense Conference of Japan, Kyoto, Dec. 4 -7. Debart, F.; Tosquellas, G.; Rayner, B.; Imbach, J.-L. Bioorg. Med. Chem. Lett. 1994, 4, 1041-1046. Koga, M.; Wilk, Α.; Moore, M. F.; Scremin, C. L.; Zhou, L.; Beaucage, S. L. J. Org. Chem. 1995, 60, 1520-1530. Boiziau, C.; Debart, F.; Rayner, B.; Imbach, J.-L.; Toulmé, J.-J. FEBS Lett. 1995, 361, 41-45. Germann, M. W.; Aramini, J. M.; Kalisch, B. W.; Pon, R. T.; van de Sande, J. H. Nucleosides Nucleotides 1997, in press. Paoletti, J.; Bazile, D.; Morvan, F.; Imbach, J.-L.; Paoletti, C. Nucleic Acids Res. 1989,17,2693-2704. Aramini, J. M.; Kalisch, B. W.; Pon, R. T.; van de Sande, J. H.; Germann, M. W. Biochemistry 1996, 35, 9355-9365. Aramini, J. M.; van de Sande, J. H.; Germann, M. W. Biochemistry 1997, 36, 9715-9725. Marky, L. Α.; Blumenfeld, K. S.; Kozlowski, S. Α.; Breslauer, K. J. Biopolymers 1983, 22, 1247-1257. Germann, M. W.; Kalisch, B. W.; van de Sande, J. H. Biochemistry 1988, 27, 8302-8306. Wüthrich, K. NMR of Proteins and Nucleic Acids, John Wiley & Sons, Inc., New York, 1986. Rinkel, L. J.; Altona, C. J. Biomol. Struct. Dyn. 1987, 4, 621-649. van Wijk, J.; Huckriede, B. D.; Ippel, J. H.; Altona, C. Methods Enzymol. 1992, 211, 286-306. Widmer, H.; Wüthrich, K. J. Magn. Reson. 1987, 74, 331-336. Schmitz, U.; James, T. L. Methods Enzymol. 1995, 261, 3-44. Gonzalez, C.; Stec, W.; Reynolds, Μ. Α.; James, T. L. Biochemistry 1995, 34, 4969-4982. Gorenstein, D. G. Chem. Rev. 1994, 94, 1315-1338. Roongta, V. Α.; Jones, C. R.; Gorenstein, D. G. Biochemistry 1990, 29, 52455258. Sklenár, V.; Miyashiro, H.; Zon, G.; Miles, T.; Bax, A. FEBS Lett. 1986, 208, 94-98. Westhof, E. J. Biomol. Struct. Dyn. 1987, 5, 581-600. Harrison, R. W. J. Comput. Chem. 1993, 14, 1112-1122. Ide, H.; Shimizu, H.; Kimura, Y.; Sakamoto, S.; Makino, K.; Glackin, M.; Wallace, S. S.; Nakamuta, H.; Sasaki, M.; Sugimoto, N. Biochemistry 1995, 34, 6947-6955. Germann, M. W.; Kalisch, B. W.; Lundberg, P.; Vogel, H. J.; van de Sande, J. H. Nucleic Acids Res. 1990, 18, 1489-1498.


Molecular Modeling of Nucleic Acids - American Chemical Society

Recommend Documents