Straightforward and Reversible Photoregulation of Hybridization by Using a Photochromic Nucleoside

Abstract

Hybridization of nucleic acids through Watson-Crick base pairing is a fundamental phenomenon in many biological events, such as gene regulation [1] by antisense agents, [2] small interfering RNA (siRNA), [3] or microRNA (miRNA). [4] In addition, the ability to form duplexes and other secondary structures through predictable hybridization has been used in constructing programmable devices and architectures on the nanometer-length scale.[5] Therefore, the necessity for methods that control hybridization by external stimuli is clear. The most promising external trigger is photoirradiation because it allows accurate and easy control of the location, dosage, and time when an event occurs. One common approach for photoregulation of hybridization involves the installation of a photoprotecting group that can be completely removed by photoirradiation.[6] This strategy, termed caging, [7] allows regulation only once and in only one direction, whereas the method employing cis-trans photoisomerization of azobenzene inserted as a base-pair (bp) replacement allows reversible control.[8] Although a significant melting-temperature difference (DT m ) is obtained upon cis-trans isomerization of azobenzene, this approach requires the introduction of multiple azobenzene moieties in the side chain. For example, 9 azobenzenes are required for the photoregulation of a 20-bp DNA duplex; these cause the structure of the duplex to deviate far from the B form and prevent its interaction with proteins. [9] Additional efforts are, therefore, needed to create more broadly applicable photoregulation methods that promise straightforward and reversible control without harm to the native B-form structure.Herein, we report a new strategy for the photoregulation of hybridization by using cis-trans photoisomerization of a photochromic nucleoside (PCN) that reversibly changes its photochemical and physical properties, such as fluorescence intensity, upon photoisomerization by an external light stimulus.[10] Our strategy successfully allowed extremely straightforward and reversible duplex regulation of a 20-bp DNA, even at room temperature. We designed three C8-substituted 2'-deoxyguanosine PCNs, G, so the stability of the duplex should change due to alteration in the steric hindrance to the backbone upon cis-trans isomerization (Scheme 1). The synthesis of the PCNs was achieved by employing two consecutive palladium-catalyzed crosscoupling reactions, as shown in Scheme 2. 8-Bromo-2'-deoxyguanosine (1) was converted into 2 by stepwise protections of the amino group with DMF-dimethylacetal and of the 5'-hydroxy group with 4,4'-dimethoxytritylchloride. Compound 2 was then subjected to cross-coupling with tributyl-

X-ray crystal structures of halogen containing nucleobase derivatives in unsolvated and DMSO solvated forms

“…In addition, the ability of nucleobases to form duplexes and other secondary structures [3] is becoming more and more widespread in the construction of new materials for potential nanotechnological applications [4][5][6][7][8][9]. With reference to this behavior, the hybridization of nucleobases with fluorophores [10,11] or metal complexes [12] has led to the creation of programmable supramolecular devices and architectures [13][14][15][16], all showing the particular interaction property of nucleobases as an important principle [17,18].…”

Fluorescent Oligonucleotides Containing a 2‐Ethynylfluorene‐ or 2‐Ethynylfluorenone‐labeled 2′‐Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation

“…We synthesized the FL ‐ and FO ‐labeled deoxyguanosine derivatives 2a and 2b from 5′‐ O ‐[bis(4‐methoxyphenyl)phenylmethyl]‐8‐bromo‐2′‐deoxy‐ N ‐[(dimethylamino)methylene]guanosine 1 using a palladium‐catalyzed Sonogashira coupling with 2‐ethynyl‐9 H ‐fluorene and 2‐ethynyl‐9 H ‐fluoren‐9‐one, respectively, followed by conversion to the corresponding phosphoramidites (Scheme ). We incorporated the FL ‐ and FO ‐labeled deoxyguanosines G FL and G FO , respectively, at the central positions of ODNs using phosphoramidite protocols of automated solid‐phase DNA synthesis .…”

“…All commercially available chemicals were used without further purification; solvents were carefully dried and distilled from appropriate drying agents prior to use. The syntheses of 1 , G FL , and G FO have been reported previously …”

Synthesis and Properties of 2'-Deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5 Position

“…Owing to their dynamic structural changes upon photo-irradiation, cis-trans type photochromic derivatives could greatly influenced the stability of nucleic acid duplexes. Although stilbene-type derivative-modified ONs have been utilized for photo-control of duplex formation, G-quadruplex formation, and gene expression, they require short wavelength photo-irradiation for cis to trans isomerization [9][10][11]. This would be disadvantageous for biomolecules due to photo-damaging reactions including the formation of pyrimidine dimers [12].…”