Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K)

Abstract

A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The non-standard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXKDNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.

Accurate Base Pair Energies of Artificially Expanded Genetic Information Systems (AEGIS): Clues for Their Mutagenic Characteristics

“…This is in agreement with an X-ray crystallography study involving the GATCXK DNA. 58 However, the X:K pair is about 3.92 kcal/mol less stable than the G:C complex and about 6.36 kcal/mol less stable than the J:V complex (Tables 1−3). Notably, the three hydrogen-bonded X:K base pair is only about 2.34 kcal/mol more stable than the two hydrogen-bonded A:T base pair (Tables 1 and 3).…”

“…However, based on the computation of gasphase free energies, the X:K pair was suggested to be less stable than the A:T pair. 58 It was argued that in the X:K pair, the N1 proton of X had transferred to the N3 of K, thereby producing a X(−H + ):K(+H + ) pair. 58 However, we could not find any spontaneous proton transfer in the X:K pair that may give rise to the X(−H + ):K(+H + ) pair.…”

Artificially Expanded Genetic Information Systems for New Aptamer Technologies

“…The development of AEGIS was supported by synthetic chemistry [ 78 ], mechanistic chemistry [ 79 ], enzymology [ 80 ], protein engineering [ 81 ], structural biology [ 82 , 83 , 84 ], and natural Darwinism [ 85 , 86 , 87 , 88 , 89 , 90 ]. Here, these worked together to not only improve AEGIS, but also to lead to a deeper understanding of how natural genetic biopolymers work.…”

“…In DNA, the crystal structure of a single Z:P pair likewise showed no substantial deviation from Watson–Crick geometry [ 93 ]. Indeed, duplexes with two or six Z:P pairs retain their overall Watson–Crick geometry [ 82 , 84 ] ( Figure 2 , left).…”

An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells

“…Available structures of DNA containing P : Z pairs show that they distort the standard duplex structure very little. Indeed, the A:T pair, joined by only two hydrogen bonds, provides a greater distortion …”