A New Model for the K⁺-Induced Macromolecular Structure of Guanosine 5‘-Monophosphate in Solution

Abstract

The 31 P NMR spectra of (TMA) 2 (5′-GMP), where TMA is [(CH 3 ) 4 N] + and 5′-GMP is guanosine 5′-monophosphate, and K 2 (5′-GMP), containing various amounts of KCl or TMACl, have been obtained at 2 °C. Variable-temperature spectra have also been obtained for K 2 (5′-GMP). The TMA + ion serves to neutralize the charge on the dianionic 5′-GMP and permits the added K + to bond preferentially in structureforming sites. 1 H NMR spectra (one-and two-dimensional) have been obtained for K 2 (5′-GMP) and used to assign the proton resonances in the self-associated structures and determine that all residues have the anti glycosidic conformation. The 31 P and 1 H NMR spectra are very complex and indicate the presence of a large number of molecular environments and a structural variation dependent upon the mole ratio of 5′-GMP to K + . A new model for the solution structure is proposed in which the 5′-GMP forms a pseudofour-stranded helix with guanine-guanine hydrogen bonding forming a continuous helical strand, rather than the usual planar G-tetrad structure. The guanine-guanine hydrogen bonding sites are the same as that found in a G-tetrad. The K + ions would be located in the center of the helix and bonding to the carbonyl oxygens. They are interacting with the phosphates as well. Integration data from the largest sized species give an estimate of 14.3 ( 1.1 residues in a helical structure.

The Effect of Temperature on the Self-Assembly of Deoxyguanosine 5'-Monophosphate in Pretransitional Region of the I-Ch Phase Transition

“…Previous 31 P NMR measurements revealed that at T ¼ 25 C only 13.6% of the molecules are involved into the formation of columnar stacks [4]. Temperature dependent ''melting'' behavior of guanosine stacks has been also observed by other experimental methods, for example NMR spectroscopy [7][8][9], interferometric DLS [10], X-ray and circular dichroism spectroscopy [11][12][13][14], and is in agreement with out observations.…”

Guanine-Centric Self-Assembly of Nucleotides in Water: An Important Consideration in Prebiotic Chemistry

“…It has been observed that the proportion of helix to G4 increases with increasing K + (Hightower et al, 2009). Additionally, the structure of the tetrads in the two salts is different (Hightower et al, 2009); in Na + the tetrads alternate between C3¢-endo (anti) and C2¢-endo (syn) sugar conformations (Wu and Kwan, 2009), while in K + they are all anti, consistent with a parallel arrangement or a continuous helix (Walmsley and Burnett, 1999). Interestingly, the solutions of GMPdss with NaH 2 PO 4 and KH 2 PO 4 tend to establish the low and high ends, respectively, of thermal stability and CD shape and peak magnitude, which bracket the solutions of GMPdss/XMPfa (with the exception of X = G).…”

“…It is not surprising that Na + and K + would favor different structures. Na + is smaller than K + and fits into the center of a single tetrad, whereas the larger K + occupies the space between two tetrads (Walmsley and Burnett, 1999;Panda and Walmsley, 2011). Another consideration is the competition between G-tetrads and the continuous helix, which is promoted by K + (Walmsley and Burnett, 1999), although it may also occur in the presence of Na + (Sasisekharan et al, 1975).…”

“…In the case of GMP, an alternate structure in which the guanines are associated with each other in a continuous helix rather than discrete tetrads has been reported to form in the presence of K + (Walmsley and Burnett, 1999). Higher-order G-tetrad assemblies and gel phases have also been observed in solutions containing mixtures of G-tetrad-forming compounds such as GMP and guanosine (Yu et al, 2008;Novotná et al, 2012;Lokesh and Suryaprakash, 2013) and GMP and isoguanosine phosphate (Roberts et al, 1997).…”

Cyclic Tetranuclear and Hexanuclear Palladium(II) Complexes and Their Host−guest Chemistry

“…Although it might seem more reasonable for the TMA + ion to interact with the negative phosphate groups, it is known that the interaction of this cation with 5′AMP and 5′GMP is electrostatic only 42 and that it does not affect the phosphate chemical shift in aqueous solution. 43 On the other hand, the tetrabutylammonium ion did not bond at all; apparently it is too large to fit in the cavity.…”