Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Lee, Chewook; Park, Kwang Hee; Cho, Minhaeng

doi:10.1063/1.2213257

Cited by 75 publications

(116 citation statements)

References 79 publications

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“…For these highly flexible single strands coiling is expected, so a preferential orientation or specific tilt angle is not likely. Even for better organized layers of shorter DNA, the orientation could not be deduced based on IR SE alone, due to the complexity of the bands in the 'amide I' band (related to vibrations of amino and carbonyl groups [89,90]). …”

Section: Ir and Uv Ellipsometrymentioning

confidence: 99%

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

Wenmackers

Vermeeren

vandeVen

et al. 2009

Physica Status Solidi (a)

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This article reviews the current state‐of‐the art of diamond‐based DNA sensors. Some general concepts involved in biosensors are introduced and applied to DNA sensors. The properties of chemically vapor deposited (CVD) diamond relevant for this application are summed up, with special attention for the stability and bio‐compatibility of the material. Several routes to functionalize the diamond surface are considered. The physical properties of the obtained DNA layers are discussed in terms of surface density and molecular conformation. Possible read‐out strategies are evaluated, including optical and electronic sensing. With diamond‐based DNA sensors, real‐time and label‐free sensing is achieved. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

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Section: Ir and Uv Ellipsometrymentioning

confidence: 99%

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

Wenmackers

Vermeeren

vandeVen

et al. 2009

Physica Status Solidi (a)

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“…concentration, pH, ionic strength and temperature), hence allowing us to reproduce the physiologic medium. 21,22 Inelastic…”

mentioning

confidence: 99%

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

et al. 2013

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A full conformational study of solid-state anhydrous adenine is reported, using vibrational spectroscopy techniques coupled to DFT calculations, for the isolated molecule and the solid. In both cases, the N9H-amino tautomer was found to be the predominant species, followed by the N7H-amino form. An excellent agreement was achieved between experiment and theory, both for wavenumbers and intensities (without the need for scaling). A complete spectral assignment was performed, since all vibrational spectroscopic techniques were available to this study -FTIR, Raman and INS -allowing us to detect and interpret even the lowest frequency vibrational bands, not previously accessed. The quantum mechanical calculations presently carried out represent the highest theoretical level applied so far to the study of nucleobases.

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“…In the ground state these bands correspond to vibrations of the carbonyl bond, ring double bond stretches and NH 2 bending vibration. 18,24 The simplicity of this transient spectrum may be due to a variety of structural and electronic changes. Such changes may result from the destruction of the p-conjugated bonding network in the dCyd atomic frame causing loss of IR activity in this spectral region.…”

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confidence: 99%

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

et al. 2007

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A strong infrared band at 1574 cm 21 is observed following 267 nm excitation of 29-deoxycytidine (t = 37 ¡ 4 ps) or 29-deoxycytidine 59-monophosphate (t = 33 ¡ 4 ps); this band is provisionally attributed to an 1 n N p* state and is absent for cytosine.The nature of the electronic excited states of DNA continues to be a focus of significant interest because of their role in UV-light induced modifications that could potentially be mutagenic. 1 The nucleobases fluoresce extremely weakly and this has led to the conclusion that their excited states must be very short-lived. 2 This is supported by femtosecond transient visible absorption 3 and fluorescence upconversion 4 measurements that reveal that the bases and mononucleotides possess sub-picosecond excited state lifetimes. However, the reasons for the short lifetimes are still a matter of debate, with theoretical studies emphasising the importance of ultrafast non-radiative processes. 5 IR methods, including 2D-IR, are proving an increasingly valuable tool for the study of DNA systems. 6,7 Time-resolved IR (TRIR) absorption spectroscopy 8 can provide structural as well as kinetic information on the ultrafast processes in DNA and our first paper in this area allowed the observation of the vibrationally excited ground states formed from nucleotides excited at 267 nm. 9 Subsequently the method has been used to identify the products of the photoionisation of GMP after excitation at 200 nm 10 and very recently the formation of thymine dimers. 11 In this paper we probe the transient species formed from 29-deoxycytidine 59-monophosphate (dCMP), 29-deoxycytidine (dCyd) and cytosine (Cyt) using vibrational spectroscopy. The presence of a new short-lived species is shown for both dCyd and dCMP but not for the nucleobase Cyt. Fig. 1 shows the transient IR difference spectra recorded between 2 ps and 1000 ps after 267 nm (150 fs) excitation of the mononucleotide dCyd in neutral (buffered pH 6.9) solution. (Identical spectra were also recorded at pH 8.5). The spectrum shows areas corresponding to ground state depletion (bands at 1505, 1524, 1617 and 1652 cm 21 as found in the FTIR) and ones where the transient absorbs more strongly. Similar behaviour is observed for dCMP (see ESI).The transient decay (and the ground state recovery) is essentially complete over the 1000 ps time scale of the experiment. However, in contrast to the results for other nucleotides such as dAMP and dGMP, 9 the kinetics are distinctly biphasic (see Fig. 2). At short times (2-8 ps -shown in red in Fig. 1) the transient absorption bands are observed to shift to higher wavenumber, behaviour which is consistent with relaxation of vibrationally excited ground states, as previously proposed. 9 The time constant for this is determined to be 2.6 ¡ 0.3 ps for dCyd.After this cooling process is complete a strong transient absorption at 1574 cm 21 persists. This band is the only one observable in the IR absorption spectrum in the region 1450-1750 cm 21 (assuming that there is no accidental overlap of other band...

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Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Cited by 75 publications

References 79 publications

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

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