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Department of Bioorganic Chemistry

The Concept of Stereoelectronic Effects in DNA and RNA

("The Uppsala Stereoelectronic Effect")

The Intramolecular Stereoelectronic Forces have been found to be one of the major participants in governing the DNA and RNA self-assembly process

For a review see: "Stereoelctronic effects in nucleosides and nucleotides and their structural implications" by Thibaudeau, Acharya, and Chattopadhyaya, ISBN 91-506-1351-0. Click here to download the Monograph.

Highlight: One single atom substitution in a self-complementary 12mer DNA (O4'-oxygen in a pentose moeity by a CH2-group in cyclopentane counterpart) forces the duplex to adopt a Hoogsteen basepaired duplex, which is in equlibrium (ca 1:1) with the Watson-Crick basepaired counterpart (see PDF:320)

The intrinsic dynamic and architectural flexibility of DNA and RNA, resulting in to specific function, are the result of cooperative interplay of pentofuranose, nucleobase and phosphodiester moieties. We have earlier shown [see list of publications in http://www.boc.uu.se/] that the interplay of various stereoelectronic gauche and anomeric and associated steric effects energetically drive the sugar-phosphate conformation, which, in turn, is dictated by the electronic nature of the aglycone and other substituents of the sugar ring. Following three independent sets of experiments show that the stereoelectronic forces indeed play a significant role in the transmission of conformational information in DNA and RNA beside stacking, H-bonding and electrostatics:

(1) Using guanosine 3',5'-bis-ethylphosphate as a model mimicking the central nucleotide moiety in a trinucleoside diphosphate in a single stranded RNA (i.e. in complete absence of any intramolecular base-base stacking), we have shown that a complete interdependency of conformational preference of sugar and phosphate backbone exists in ribonucleoside 3'-ethylphophate as the of protonation-deprotonation equilibrium of the aglycone changes as a function of pH. It has been shown that the mechanism of intramolecular conformational transmission is simply governed by appropriate overlap of donor-acceptor orbitals dictated by the electronegativity of various sugar substituents [Angew Chem. Int. Ed. 38, 3645-3650 (1999) (PDF:301).; J. Phys. Org. Chem., 13, 300-305 (2000) (PDF:310)].

(2) A single-point substitution of the O4'-oxygen by a CH2 group at the sugar residue of A6 (i.e. 2'-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5'- d(C1 G2 C3 G4 A5 A6 T7 T8 C9 G10 C11 G12)2-3', has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A) to a doubly A6:T7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A) (1B): Keq = k1/k-1 = 0.56 ± 0.08 [k1 (298K) = 3.9 ± 0.8 sec-1; DH° = 164 ± 4 kJ/mol; -TDS° (298K) = -92 kJ/mol giving a of 72 kJ/mol. Ea (k1) = 167 ± 14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0 ± 0.6 sec-1, DH° = 153 ± 13 kJ/mol; -TDS (298K) = -82 kJ/mol giving a of 71 kJ/mol. Ea (k-1) = 155 ± 13 kJ/mol]. A comparison of of the forward (k1) and backward (k-1) conversions, (1A) (1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex [J. Biomolecular Struct & Dyn, 18, 783, 2001 (PDF:320)].

(3) Finally, the sensitivity of the RNase H has been explored to map the local structural changes in the antisense oligo (AON)/RNA hybrids, containing a single 1-(1',3'-O-anhydro-b-D- psicofuranosyl)thymine with locked 3'-endo sugar conformation at different sites of AON. This has revealed that the local conformational changes brought by the constrained nucleoside, although invisible by CD (global structure unaltered from that of the native counterpart), span in the hybrid as far as 5 nucleotides toward the 5'-end of the AONs (3'-end of RNA), showing the unique transmission of the structural distortion from a single modification site [Tetrahedron Letters, 41, 8601 (2000), (PDF:313, 315, 329)]].

Thermodynamic characteristics of Stereoelectronic Effects

For a review see: "Stereoelctronic effects in nucleosides and nucleotides and their structural implications" by Thibaudeau, Acharya, and Chattopadhyaya, ISBN 91-506-1351-0. Click here to download the Monograph.

We are the first to estimate its thermodynamic characteristics of the two-state C3'- endo-C2'-exo (North) C3'-exo-C2'-endo (South) equilibrium of the pentofuranose sugar in nucleosides and nucleotides, which has enabled us for the first time to quantify the thermodynamics of the stereoelectronic gauche and anomeric effects in nucleosides and nucleotides. This should have enormous importance in (i) undestanding the physico- chemical roles of different constituents of nucleic acids as well as their response to the local change of microenvironment (ii) the structure-function activity of modified nucleic acids in order to design antisense oligonucleotide, triplexing agent and specific enzyme inhibitors and (iii) reparametrization of the molecular mechanics force field for molecular modeling.

We have recently found that the energy of the protonation/deprotonation equilibrium of the heterocyclic aglycone is transmitted through the anomeric effect to drive the North South equilibrium of the pentose sugar in nucleosides and nucleotides [Ref. 253 in the publication list]. Our latest work [Refs. 301, 310] has uniquely shown a complete interdependency of conformational preference of sugar and phosphate backbone as the protonation deprotonation equilibrium of the aglycone changes as a function of pH in a mimicking model for trinucleoside diphosphate in absence of any intramolecular base-base stacking.

This tunable transmission in trinucleoside diphosphate mimic, which has been observed compared to their abasic counterpart, is observed to be much stronger at the 3'- phosphate backbone compared to its 5'-end justifies RNA as "molecular wire". Further, these studies have clearly showed that any change of the aromatic property of any specific nucleobase in the DNA or RNA by metal ion binding, H-bonding, protonation- deprotonation, alkylation, oxidation or reduction would orchestrate a profound change on the local structure of DNA or RNA by transmission of the energetics of the altered aromatic character of the heterocyclic aglycone to steer the sugar-phosphate backbone conformation through the tuning of the strength of anomeric effects in both DNA and RNA (energy pump).

Anthranilic acid charged yeast tRNAPhe or E. coli tRNAVal are able to form a stable complex with EF-Tu*GTP, hence the 2'- and 3'-O-anthraniloyladenosines and their 5'-phosphate counterparts have been conceived to mimic aminoacyl-tRNA. Since the 3'- O-anthraniloyladenosine derivative also binds more efficiently to EF-Tu*GTP complex compared to its 2'-isomer, we delineated [PDF 298] the stereoelectronic features that dictate the conformation of 3'-O-anthraniloyladenosine vis-à-vis their 2'-counterparts as well as addressed how their structures and thermodynamic stabilizations are different from adenosine.

The fact that by simply changing the electronic nature of a substituent at any of the easily accessible chiral centers (i.e. at C1', C2' or C3') one can easily change the sugar conformation (Gauche and Anomeric engineering, for recent publications see [228], [230], [231], [238], [239] and [255]), which, in turn, will have considerable impact in the engineering of the sugar/phosphate backbone conformation in the knowledge-based design of nucleic acid mimics for antisense or triplex research [see list of publications in http://www.boc.uu.se/]. Moreover, our NMR studies have also shown (i) interaction of the 2'-hydroxyl group with the vicinal phosphate moiety in RNA [252], (ii) the tunable transmission of the aromatic character of aglycone through anomeric effect in C-nucleosides [PDF 266], (iii) larger medium dependent flexibility of natural b-D-nucleosides in comparison to a-D-nucleosides [PDF 268] as well as (iv) development of new generalized Karplus equation for H-C-C-F torsions which are of fundamental interest in calculating the conformational aspects of biologically important fluorinated nucleos(t)ides [PDF 281]. Further, our high level ab initio studies [322] goes hand in hand with the NMR based experimental observations [231] of 3'-substituent dependent gauche effect in 3'- substituted 2',3'-dideoxy nucleosides.

Further work is in progress (i) to use the principles of stereoelectronic forces to engineer the geometry of nucleic acid mimics, and thereby dictate the dynamics, kinetics and thermodynamics of their binding to the target nucleic acids, (ii) hydration properties of 2'-hydroxyl group in nucleos(t)ides which will have impact on their biological function, (iii) sugar and aglycone conformation dependent differential base-pairing activity and their structural effect in helical pattern of nucleic acids and (iv) ab initio studies in order to understand the molecular mechanism of gauche and anomeric effect in nucleosides.

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