yDNA: A New Geometry for Size‐Expanded Base Pairs

Abstract

Previous studies have explored whether it is possible to replace the information-encoding part of DNA-the bases and base pairs-with other molecular replacements, and whether such new base pairs might function in recognition and in replication processes, two of the defining characteristics of the natural genetic system. [1][2][3][4][5][6] Many of these studies have been aimed at designing base pairs that can function within the content of the natural genetic system, for expansion of natures genetic alphabet. However, recent studies have moved beyond the purine-pyrimidine framework of the natural system. Examples of this new approach include metal-bridged base pairs, [4] nonpolar base pairs, [2,4] and pairs containing more than the three different types of hydrogen bonds found in nature. [5] We recently adopted a different strategy and described a molecular design in which the dimensions of the natural pairs are stretched by insertion of a benzene ring into the natural heterocycles, thus rendering base pairs 2.4 wider than the natural ones.[6] Such broad alterations of the natural design are not necessarily expected to be compatible with the natural genetic system. Rather, such studies are useful as a test of researchers understanding of how genetic systems function in general, and they may also lead to useful new applications in biotechnology and in selfassembling nanostructures.Herein we evaluate whether size-expansion of DNA base pairs can be carried out using a new geometry. Our previous design of expanded DNA-like bases (xDNA) involved a linear extension of pyrimidines and purines by addition of a benzene ring to each of the four DNA base heterocycles. [6] However, examination of models suggested that at least one other design strategy involving benzohomologation also appeared to allow for reasonable base-pair geometries and stacking with neighboring pairs. This new design, termed "yDNA" (an abbreviated form of "wide DNA"; Scheme 1) involves a different extension vector, but yields a similar degree of perturbation from the framework formed by the natural pair. Analogous designs for the other three nucleobases can be envisioned (not shown). In this initial study we tested the concept with one example, that of the expanded adenine base analogue (yA) and the corresponding deoxyriboside (dyA), both of which were previously unknown.We developed a synthetic route to prepare the phosphoramidite derivative of the new nucleoside analogue dyA in 10 steps (6 % overall yield on a gram scale, Scheme 2). Methylation of indole 1 at the 5 position was achieved by addition of three equivalents of methylmagnesium chloride to the unprotected indole 1, followed by ring oxidation to restore aromaticity. [7] The transformation of methylindole 3 [8] to indole-5-carboxaldehyde 4 was a key step; tris(dimethylamino)methane converted 3 into the enamine intermediate which was then oxidized by KMnO 4 in one pot to afford compound 4.[9] The protected 2'-deoxyriboside 7 was formed in three subsequent steps from the indole-5-aldehyde 4. Conv...

Thermodynamics of Nucleic Acid Structural Modifications for Biotechnology Applications

“…For example, base stacking depends on base size, which is an important consideration in technologies based on expanded bases such as x-and yDNA shown in Figure 1. [27][28][29] Modified nucleosides capable of photocrosslinking reactions include 4-thio and 4-halogeno derivatives of uridine of deoxyribouridine shown in Figure 2. Photocrosslinking with DNA or DNA/RNA strands depends on appropriate conformations, which are accessible transiently in DNA, and hence is dependent on the dynamics of the structure.…”

Self‐Replication in Chemistry and Biology

“…In the most striking example, the natural nucleosides have been redesigned with an expanded size by incorporation of a phenyl group between the sugar and the hydrogenbonding ring [51,[61][62][63]. This size expanded system, termed xDNA (x for expanded) (Fig.…”

“…Because the base-pairing is not altered, x, y DNA are still capable of base-pairing with DNA and RNA but forming double helices with an expanded diameter and higher stability due to the increased stacking of the expanded bases [62,66]. Finally, orthogonality might simply be semantic in that genetic information encoded in such a way that it is ''meaningless'' to the cellular host, unless specific transliterases are provided.…”

Highlights in Organic Chemistry [Modification of Nucleoside Heterocycles to Probe and Expand Nucleic Acid Structure and Function]

“…Most importantly, polymerases, ligases, kinases, and even the ribosomes recognize the artificial nucleosides, which allowed Benner and co-workers to develop Artificially Expanded Genetic Information Systems (AEGIS) based on the non-natural nucleobases [5]. Kool and co-workers [7,8] recently designed new base pairing systems using the Watson-Crick hydrogen-bonding scheme between heterocycles that are 2.4 Å wider than those of natural DNA (Scheme 2). Although the size-expanded nucleosides are destabilizing in the context of natural DNA, probably because of backbone distortions, xDNA (expanded DNA) [7,9,10] and yDNA (wide DNA) [8,11] duplexes built of only the expanded base pairs are more stable than the natural DNA duplexes.…”

“…Kool and co-workers [7,8] recently designed new base pairing systems using the Watson-Crick hydrogen-bonding scheme between heterocycles that are 2.4 Å wider than those of natural DNA (Scheme 2). Although the size-expanded nucleosides are destabilizing in the context of natural DNA, probably because of backbone distortions, xDNA (expanded DNA) [7,9,10] and yDNA (wide DNA) [8,11] duplexes built of only the expanded base pairs are more stable than the natural DNA duplexes. The nucleobases of xDNA and yDNA are both designed by extension of natural nucleobases with an extra benzene ring.…”