Kiyohiko Kawai

Sequence-independent and rapid long-range charge transfer through DNA

Interest in using DNA as a building block for nanoelectronic sensors and devices stems from its efficient hole-conducting properties and the relative ease with which it can be organized into predictable nanometre-sized two- and three-dimensional structures. However, because a hole migrates along DNA through the highest occupied molecular orbital of the guanine bases, its conductivity decreases as the adenine-thymine base-pair content increases. This means that there are limitations on what sequences can be used to construct functional nanoelectronic circuits, particularly those rich in adenine-thymine pairs. Here we show that the charge-transfer efficiency can be dramatically increased in a manner independent of guanine-cytosine content by adjusting the highest occupied molecular orbital level of the adenine-thymine base pair to be closer to that of the guanine-cytosine pair. This is achieved by substituting the N7 nitrogen atom of adenine with a C-H group to give 7-deazaadenine, which does not disturb the complementary base pairing observed in DNA.

Direct Measurement of the Dynamics of Excess Electron Transfer through Consecutive Thymine Sequence in DNA

Charge transfer in DNA is an essential process in biological systems because of its close relation to DNA damage and repair. DNA is also an important material used in nanotechnology for wiring and constructing various nanomaterials. Although hole transfer in DNA has been investigated by various researchers and the dynamic properties of this process have been well established, the dynamics of a negative charge, that is, excess electron, in DNA have not been revealed until now. In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and diphenylacetylene (DPA) as an electron acceptor at both ends. The selective excitation of 4T by a femtosecond laser pulse caused the excess electron injection into DNA, and led to EET in DNA by a consecutive T-hopping mechanism, which eventually formed the DPA radical anion (DPA(•-)). The rate constant for the process of EET through consecutive T was determined to be (4.4 ± 0.3) × 10(10) s(-1) from an analysis of the kinetic traces of the ΔO.D. during the laser flash photolysis. It should be emphasized that the EET rate constant for T-hopping is faster than the rate constants for oxidative hole transfers in DNA (10(4) to 10(10) s(-1) for A- and G-hopping).

Charge transfer through DNA nanoscaled assembly programmable with DNA building blocks

DNA nanostructures based on programmable DNA molecular recognition have been developed, but the nanoelectronics of using DNA is still challenging. A more rapid charge-transfer (CT) process through the DNA nanoassembly is required for further development of programmable DNA nanoelectronics. In this article, we present direct absorption measurements of the long-range CT over a 140-Å DNA assembly based on a GC repetitive sequence constructed by simply mixing DNA building blocks. We show that a CT through DNA nanoscale assembly is possible and programmable with the designed DNA sequence.

Kinetics of charge transfer in DNA containing a mismatch

Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

Sequence dependence of excess electron transfer in DNA.

DNA-mediated charge transfer has recently received a substantial attention because of its biological relevance in the DNA damage and DNA repair as well as the potential applications to nanoscale electronic devices. In contrast to the numerous mechanistic studies on oxidative hole transfer (HT) through DNA, our understanding of reductive electron transfer process still remains limited. In this article, we demonstrate the results of direct observation of the excess electron transfer (EET) through DNA, which conjugated with aminopyrene ((A)Py) and diphenylacetylene (DPA) as a photosensitizing donor and an acceptor of excess electron, respectively. By inserting dihydrothymine as a spacer between (A)Py and T or C, the yield of electron arrival to DPA was improved. It was indicated that EET through DNA completed within a few or a few tens nanosecond time scale even for EET over 34 Å for both consecutive T and C sequences. The various factors such as mismatch sequence and DNA length on the yield of electron arrival to DPA were examined.

Synthesis of ODNs Containing 4-Methylamino-1,8-naphthalimide as a fluorescence probe in DNA

Synthesis and fluorescence properties of oligodeoxynucleotides containing 4-methylamino-1,8-naphthalimide (NI) have been described. NI was successfully incorporated into DNA without significant destabilization of DNA whilst retaining its high fluorescence quantum yield. The attachment site of the NI greatly affected its property as an energy acceptor in FRET analysis.

Long-Range Charge Transfer through DNA by Replacing Adenine with Diaminopurine

A positive charge migrates along DNA mainly via a series of short-range charge transfer (CT) processes between G-C base pairs, which have relatively high HOMO levels. As such, the CT efficiency sharply decreases with the insertion of A-T base pairs between the G-C base pairs. We have previously demonstrated that the CT efficiency through DNA can be dramatically increased by using deazaadenine (Z), an analogue of A, to adjust the HOMO levels of the A-T base pairs closer to those of the G-C base pairs (Nat. Chem. 2009, 1, 156). In the present study, we have expanded this approach to show that the CT efficiency can also be increased by replacing A bases with diaminopurine (D).

Detection of the G-quadruplex-TMPyP4 complex by 2-aminopurine modified human telomeric DNA

2-Aminopurine (Ap) modified human telomere sequences were used to monitor the specific complex formation of the G-quadruplex and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4).

HOMO Energy Gap Dependence of Hole-Transfer Kinetics in DNA

DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).

Stabilization of Hoogsteen base pairing by introduction of NH2 group at the C8 position of adenine

Abstract The synthesis of 8-aminodeoxyadenosine containing oligonucleotides has been described. The incorporation of an amino group at the C8 position of adenine greatly stabilized the Hoogsteen base pairing in triplex formation.