Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

Stereochemistry of 2',5' nucleic acids and their constituents

Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that this feature is accompanied by a switch in the preferred sugar ring conformation in 3',5' and 2',5' nucleic acids. 3' ribose and 3' deoxyribose rings (in 2',5' linkages) tend to favour C2' endo and C3' endo puckers respectively in contrast to C3' endo and C2' endo puckers favored by 2' ribose and 2' deoxyribose sugars (in 3',5' linkages). The distinguishable features between the nucleotide repeats of 3',5' and 2',5' nucleic acids need to be recognised while discussing their structural properties, as well as those of a variety of complexes that could be formed involving 2',5' and 3',5' strands of DNA and RNA. Ability and stability, or lack of them, for formation of a specific combination of these complexes may be directly related to the stereochemical constraints imposed as a consequence of conformationally homogeneous or heterogeneous nature of the repeating nucleotides of the complexing chains. As a first step towards delineating stereochemical features that distinguish 2',5' nucleic acids from their naturally occurring isomer A and B type helices have been modelled using the new concept of "compact" and "extended" nucleotide repeat that seemingly unifies helix generation of both types of linkages. Helical models for 2',5' RNA with "dinucleotide" repeat based on the crystal structure of 2',5' ApU have also been obtained.

Preference for syn conformation: crystal structures of free acid and ammonium salt of adenosine 2'-monophosphate: an inhibitor of RNase T1

This paper reports the crystal structures of free acid and ammonium salt of adenosine 2'-monophosphate (2'-AMP). 2'-AMP crystallizes in the hexagonal space group P6(5)22 with a = 9.530(3) A, c = 73.422(2) A, and Z= 12. 2'-AMP.NH4 crystallizes in the trigonal space group P3(1) with a = 9.003(2) A, c = 34.743(2) A and Z= 6. Both the structures were solved by direct methods and refined by full matrix least- squares method to final R factors of 0.080 and 0.038 for 2'-AMP and 2'-AMP.NH4 respectively. The adenine bases of both the structures are in syn conformation contrasting with the anti geometry in 3'-AMP, 5'-AMP and the enzyme bound state. Ribose moiety of 2'-AMP is in C2' -endo conformation. However, the ribose moieties of both the nucleotide molecules display C2'-endo-C3'-exo twist conformation in 2'- AMP.NH4 structure. Both structures demonstrate g+ conformation about C4' -C5' bond. 2'-AMP and one of the nucleotide molecules of 2'-AMP.NH4 are protonated at N1 and the ammonium ion is involved in a bifurcated hydrogen bond with O3' B and O3A atoms. A characteristic feature of both the structures is the intramolecular O5' -N3 hydrogen bond. Our crystallographic results on 2'-AMP corroborates the earlier conclusion that the enzyme-bound state is not the lowest energy state of this nucleotide. 2' -AMP displays base-ribose 04' stacking not seen in the 2'-AMP.NH4 structure. Theoretical and experimental studies on 2'-, 3'- and 5'-AMP structures have been discussed.

Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.

Conformational and stacking properties of 3'-5' and 2'-5' linked oligoribonucleotides studied by CD

Comparative CD studies have been carried out to characterize the properties of 2'-5' and 3'-5' oligoriboadenylates and oligoribouridylates from dimer to decamer. The CD band of the 3'-5' oligoribonucleotides was larger than that of the 2'-5' oligoribonucleotides and increased with the increase in chain length, while the CD band of the 2'-5' oligoribonucleotides increased little beyond the dimer level. The CD analysis of the chain length dependency revealed that the 3'-5' oligoribonucleotides adopt mainly the base-base stacking interaction, while the base-sugar interaction is predominant in the 2'-5' oligoribonucleotides. The CD intensity of 3'-5' oligoribonucleotides decreased to a larger extent at elevated temperatures or in the presence of ethanol compared to that of the 2'-5' counterparts. Mg2+ or Mn2+ ion enhanced the magnitude of the CD of 3'-5' octariboadenylate, while a small decrease in the CD was observed by the presence of Mg2+ or Mn2+ ion to the 2'-5' octariboadenylate. The 3'-5' oligoribonucleotide is likely conformationally flexible and can form helical ordered structure with strong base-base stacking depending on changes in the environment such as temperature the presence of Mg2+ ion, or hydrophobicity of the solution.

Finding and visualizing nucleic acid base stacking

Base stacking is one of the primary factors stabilizing nucleic acid structure. Yet, methods for locating stacking interactions in DNA and RNA are rare and methods for displaying stacking are rarer still. We present here simple, automated procedures to search nucleic acid molecules for base-base and base-oxygen stacking and to display these interactions graphically in a manner that readily conveys both the location and the quality of the interaction. The method makes no a priori assumptions about relative base positions when searching for stacking, nor does it rely on empirical energy functions. This is a distinct advantage for two reasons. First, the relative contributions of the forces stabilizing stacked bases are unknown. Second, the electrostatic and hydrophobic components of base stacking are both poorly defined by existing potential energy functions.