A cytosine analogue capable of clamp-like binding to a guanine in helical nucleic acids
A cytosine analogue capable of clamp-like binding to a guanine in helical nucleic acids
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DOI：
10.1021/ja981286z
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发表时间：
1998-08-26
影响因子：
15
通讯作者：
Matteucci, MD
中科院分区：
文献类型：
--
作者：
Lin, KY;Matteucci, MD
The Watson-Crick pairing of heterocycles within duplex DNA is the foundation of biomolecular recognition. 1 The cytosineguanine interaction is formed by three hydrogen bonds. The guanine base contains two unused hydrogen bond acceptors in the major groove at the O6 and N7 of the Hoogsteen binding face. A cytosine analogue termed G-clamp, when incorporated into oligonucleotides (ODNs), simultaneously recognizes both the Watson-Crick and Hoogsteen faces of a complementary guanine within a helix. A single G-clamp analogue substitution within an ODN results in substantially enhanced helical thermal stability and mismatch discrimination when hybridized to complementary DNA and RNA. These properties of enhanced affinity and specificity are of interest in the fields of nucleic acid based diagnostics2, 3 and the sequence-specific targeting of RNA by the antisense approach. 4, 5We previously reported the synthesis and binding properties of ODNs containing the tricyclic 2′-deoxycytidine analogue, phenoxazine (structure 1, Figure 1). 6 This heterocyclic modification provided a rigid scaffold for appending groups designed to interact with the Hoogsteen binding face of a complementary basepaired guanine. Model building studies suggested that the protonated amino group of the G-clamp (structure 2, Figure 1) could make a specific hydrogen bonded contact with the O6 of the targeted guanine within a helix as shown in Figure 2. The syntheses of the monomer synthons required for ODN synthesis are reported elsewhere. 7 The ODNs shown in Table 1 were synthesized and purified by standard methods8 and characterized by MALDI-TOF mass spectrometry. The ODNs were hybridized to a complementary ODN and Tm measurements recorded. The data are shown in Table 1. Only the G-clamp containing ODN showed dramatically enhanced affinity relative to a 5-methyl cytosine control. The tricyclic phenoxazine 1 bearing no arm showed affinity enhancement consistent with the improved stacking interactions observed previously. 6 The virtually isosteric tricyclic analogue 3 bearing the weakly hydrogen-bond-donating hydroxyl group showed no enhanced affinity. 9 The acyclic derivative 4 lacking the conformational restriction of G-clamp demonstrated no enhanced affinity. 11 The G-clamp’s dramatic affinity for the complementary guanine depended on the appropriate positioning of the strong hydrogen bond donor. A specific interaction with the Hoogsteen face of the targeted guanine should result in enhanced specificity. The G-clamp possessed greater discrimination between the perfect match with guanine and mismatches with adenine, thymine, and cytosine. The matrix of matched and mismatched Tm values are shown in Table 2. The G-clamp conferred enhanced specificity in all cases relative to 5-methyl cytosine and the parent phenoxazine 1. Only the specific hybridization with a targeted guanine resulted in enhanced affinity.
