PICOSECOND FLUORESCENCE DECAY TIME MEASUREMENTS OF NUCLEIC ACIDS AT ROOM TEMPERATURE IN AQUEOUS SOLUTION

Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy

Methylated DNA/RNA nucleobases are important epigenetic marks in living species and play an important role for targeted therapies. Moreover, they could bring significant changes to the photo-stability of nucleic acid, leading these sites become mutational hotspots for disease such as skin cancer. While a number of studies have demonstrated the relationship between excited state dynamics and the biological function of methylated cytosine in DNA, investigations aimed at unraveling the excited state dynamics of methylated guanosine in RNA have been largely overlooked. In this work, influence of methylation on the excited state dynamics of guanosine is studied by using femtosecond time-resolved spectroscopy. Our results suggest that the effect of methyl substitution on the photophysical properties of guanosine is position sensitive. N1-methylguanosine shows very similar excited state dynamics as that in guanosine, while almost one order of magnitude longer lifetime of the La state is observed in N2, N2-dimethylguanosine. Notably, N7-methylation can lead to a new minimum on the La state, which shows a two orders of magnitude longer excited state lifetime compared with guanosine. These findings not only help understanding excited state dynamics of methylated guanosines, but also lay the foundation for further studying DNA/RNA strands incorporated with these bases.

Compact Color Biofinder (CoCoBi): Fast, Standoff, Sensitive Detection of Biomolecules and Polyaromatic Hydrocarbons for the Detection of Life

We have developed a compact instrument called the "COmpact COlor BIofinder", or CoCoBi, for the standoff detection of biological materials and organics with polyaromatic hydrocarbons (PAHs) using a nondestructive approach in a wide area. The CoCoBi system uses a compact solid state, conductively cooled neodymium-doped yttrium aluminum garnet (Nd:YAG) nanosecond pulsed laser capable of simultaneously providing two excitation wavelengths, 355 and 532 nm, and a compact, sensitive-gated color complementary metal-oxide-semiconductor camera detector. The system is compact, portable, and determines the location of biological materials and organics with PAHs in an area 1590 cm2 wide, from a target distance of 3 m through live video using fast fluorescence signals. The CoCoBi system is highly sensitive and capable of detecting a PAH concentration below 1 part per billion from a distance of 1 m. The color images provide the simultaneous detection of various objects in the target area using shades of color and morphological features. We demonstrate that this unique feature successfully detected the biological remains present in a 150-million-year-old fossil buried in a fluorescent clay matrix. The CoCoBi was also successfully field-tested in Hawaiian ocean water during daylight hours for the detection of natural biological materials present in the ocean. The wide-area and video-speed imaging capabilities of CoCoBi for biodetection may be highly useful in future NASA rover-lander life detection missions.

OrganiCam: a lightweight time-resolved laser-induced luminescence imager and Raman spectrometer for planetary organic material characterization

OrganiCam is a laser-induced luminescence imager and spectrometer designed for standoff organic and biosignature detection on planetary bodies. OrganiCam uses a diffused laser beam (12° cone) to cover a large area at several meters distance and records luminescence on half of its intensified detector. The diffuser can be removed to record Raman and fluorescence spectra from a small spot from 2 m standoff distance. OrganiCam's small size and light weight makes it ideal for surveying organics on planetary surfaces. We have designed and built a brassboard version of the OrganiCam instrument and performed initial tests of the system.

"Standoff Biofinder" for Fast, Noncontact, Nondestructive, Large-Area Detection of Biological Materials for Planetary Exploration

We developed a prototype instrument called the Standoff Biofinder, which can quickly locate biological material in a 500 cm(2) area from a 2 m standoff distance with a detection time of 0.1 s. All biogenic materials give strong fluorescence signals when excited with UV and visible lasers. In addition, the luminescence decay time of biogenic compounds is much shorter (<100 ns) than the micro- to millisecond decay time of transition metal ions and rare-earth ions in minerals and rocks. The Standoff Biofinder takes advantage of the short lifetime of biofluorescent materials to obtain real-time fluorescence images that show the locations of biological materials among luminescent minerals in a geological context. The Standoff Biofinder instrument will be useful for locating biological material during future NASA rover, lander, and crewed missions. Additionally, the instrument can be used for nondestructive detection of biological materials in unique samples, such as those obtained by sample return missions from the outer planets and asteroids. The Standoff Biofinder also has the capacity to detect microbes and bacteria on space instruments for planetary protection purposes.

KEY WORDS

Standoff Biofinder-Luminescence-Time-resolved fluorescence-Biofluorescence-Planetary exploration-Planetary protection-Noncontact nondestructive biodetection. Astrobiology 16, 715-729.

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2-aminopurine (2AP) as an energy trap in short (3- to 20-base) single- and double-stranded DNA oligomers is reviewed. Variation of 2AP's neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3' end, (3) approximate equality of efficiencies for 3' to 5' and 5' to 3' directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de-excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross-strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below -60 degrees C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single-stranded DNA, are separated by less than 5 A (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor-acceptor distance, the experimental dependence clearly disagrees with Förster 1/r6 dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base-base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular "fiber optic" face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this "fiber optic" a challenge.

Radiative decay engineering: the role of photonic mode density in biotechnology

Fluorescence detection is a central technology in biological research and biotechnology. A vast array of fluorescent probes are available with diverse spectral properties. These properties were 'engineered' into fluorophores by modification of the chemical structures. Essentially, all present uses of fluorescence rely on the radiation of energy into optically transparent media, the free space which surrounds the fluorophores. In this paper, we summarize an opportunity for novel fluorescence technology based on modification of the photonic mode density around the fluorophore and thus control of its spectral properties. This modification can be accomplished by proximity of fluorophores to metallic particles of gold, silver and possibly others. By engineering the size and shape of the metal particles, and the location of the fluorophores relative to the surfaces, fluorophores can be quenched, display increases in quantum yield, and changes in lifetime. Fluorophore-metal surface combinations can even display directional rather than isotropic emission. We describe recent experimental results and suggest potential biomedical applications of fluorophore-metal particle interactions.

Radiative decay engineering. 2. Effects of Silver Island films on fluorescence intensity, lifetimes, and resonance energy transfer

Metallic surfaces can have unusual effects on fluorophores such as increasing or decreasing the rates of radiative decay and the rates of resonance energy transfer (RET). In the present article we describe the effects of metallic silver island films on the emission spectra, lifetimes, and energy transfer for several fluorophores. The fluorophores are not covalently coupled to the silver islands so that there are a range of fluorophore-to-metal distances. We show that proximity of fluorophores to the silver islands results in increased fluorescence intensity, with the largest enhancement for the lowest-quantum-yield fluorophores. Importantly, the metal-induced increases in intensity are accompanied by decreased lifetimes and increased photostability. These effects demonstrate that the silver islands have increased the radiative decay rates of the fluorophore. For solvent-sensitive fluorophores the emission spectra shifted to shorted wavelengths in the presence of the silver islands, which is consistent with a decrease of the apparent lifetime for fluorophores near the metal islands. We also observed an increased intensity and blue spectral shift for the protein human glyoxalase, which displays a low quantum yield for its intrinsic tryptophan emission. In this case the blue shift is thought to be due to increased emission from a buried low-quantum-yield tryptophan residue. Increased intensities were also observed for the intrinsic emission of the nucleic acid bases adenine and thymine and for single-stranded 15-mers poly(T) and poly(C). And finally, we observed increased RET for donors and acceptors in solution and when bound to double-helical DNA. These results demonstrate that metallic particles can be used to modify the emission from intrinsic and extrinsic fluorophores in biochemical systems.

Radiative decay engineering: biophysical and biomedical applications

Fluorescence spectroscopy is a widely used research tool in biochemistry and molecular biology. Fluorescence has also become the dominant method enabling the revolution in medical diagnostics, DNA sequencing, and genomics. To date all the fluorescence observables, including spectral shifts, anisotropies, quantum yields, and lifetimes, have all been utilized in basic and applied uses of fluorescence. In this forward-looking article we describe a new opportunity in fluorescence, radiative decay engineering (RDE). By RDE we mean modifying the emission of fluorophores or chromophores by increasing or decreasing their radiative decay rates. In most fluorescence experiments the radiative rates are not changed because these rates depend on the extinction coefficient of the fluorophore. This intrinsic rate is not changed by quenching and is only weakly dependent on environmental effects. Spectral changes are usually caused by changes in the nonradiative rates resulting from quenching or resonance energy transfer. These processes affect the emission by providing additional routes for decay of the excited states without emission. In contrast to the relatively constant radiative rates in free solution, it is known that the radiative rates can be modified by placing the fluorophores at suitable distances from metallic surfaces and particles. This Review summarizes results from the physics literature which demonstrate the effects of metallic surfaces, colloids, or islands on increasing or decreasing emissive rates, increasing the quantum yields of low quantum yield chromophores, decreasing the lifetimes, and directing the typically isotropic emission in specific directions. These effects are not due to reflection of the emitted photons, but rather as the result of the fluorophore dipole interacting with free electrons in the metal. These interactions change the intensity and temporal and spatial distribution of the radiation. We describe the unusual effects expected from increases in the radiative rates with reference to intrinsic and extrinsic biochemical fluorophores. For instance, the decreased lifetime can result in an effective increase in photostability. Proximity to nearby metallic surfaces can also increase the local field and modify the rate of excitation. We predict that the appropriate localization of fluorophores near particles can result in usefully high emission from "nonfluorescent" molecules and million-fold increases in the number of photons observable from each fluorophore. We also describe how RDE can be applied to medical testing and biotechnology. As one example we predict that nearby metal surfaces can be used to increase the low intrinsic quantum yields of nucleic acids and make unlabeled DNA detectable using its intrinsic metal-enhanced fluorescence.

DNA excited-state dynamics: ultrafast internal conversion and vibrational cooling in a series of nucleosides

To better understand DNA photodamage, several nucleosides were studied by femtosecond transient absorption spectroscopy. A 263-nm, 150-fs ultraviolet pump pulse excited each nucleoside in aqueous solution, and the subsequent dynamics were followed by transient absorption of a femtosecond continuum pulse at wavelengths between 270 and 700 nm. A transient absorption band with maximum amplitude near 600 nm was detected in protonated guanosine at pH 2. This band decayed in 191 +/- 4 ps in excellent agreement with the known fluorescence lifetime, indicating that it arises from absorption by the lowest excited singlet state. Excited state absorption for guanosine and the other nucleosides at pH 7 was observed in the same spectral region, but decayed on a subpicosecond time scale by internal conversion to the electronic ground state. The cross section for excited state absorption is very weak for all nucleosides studied, making some amount of two-photon ionization of the solvent unavoidable. The excited state lifetimes of Ado, Guo, Cyd, and Thd were determined to be 290, 460, 720, and 540 fs, respectively (uncertainties are +/-40 fs). The decay times are shorter for the purines than for the pyrimidine bases, consistent with their lower propensity for photochemical damage. Following internal conversion, vibrationally highly excited ground state molecules were detected in experiments on Ado and Cyd by hot ground state absorption at ultraviolet wavelengths. The decays are assigned to intermolecular vibrational energy transfer to the solvent. The longest time constant observed for Ado is approximately 2 ps, and we propose that solute-solvent H-bonds are responsible for this fast rate of vibrational cooling. The results show for the first time that excited singlet state dynamics of the DNA bases can be directly studied at room temperature. Like sunscreens that function by light absorption, the bases rapidly convert dangerous electronic energy into heat, and this property is likely to have played a critical role in life's early evolution on earth.

Intrinsic fluorescence from DNA can be enhanced by metallic particles

High sensitivity detection of DNA is essential for genomics. The intrinsic fluorescence from DNA is very weak and almost all methods for detecting DNA rely on the use of extrinsic fluorescent probes. We show that the intrinsic emission from DNA can be enhanced many-fold by spatial proximity to silver island films. Silver islands are subwavelength size patches of metallic silver on an inert substrate. Time-resolved measurements show a decreased lifetime for the intrinsic DNA emission near the silver islands. These results of increased intensity and decreased lifetime indicate a metal-induced increase in the radiative rate decay of the DNA bases. The possibility of increased radiative decay rates for DNA bases and other fluorophores suggest a wide variety of DNA measurements and other biomedical assays based on metal-induced increases in the fluorescence quantum yield of weakly fluorescent substances.

Sequence dependence of energy transfer in DNA oligonucleotides

The sequence, temperature, concentration, and solvent dependence of singlet energy transfer from normal DNA bases to the 2-aminopurine base in synthesized DNA oligomers were investigated by optical spectroscopy. Transfer was shown directly by a variable fluorescence excitation band at 260-280 nm. Adenine (A) is the most efficient energy donor by an order of magnitude. Stacks of A adjacent to 2AP act as an antenna for 2AP excitation. An interposed G, C, or T base between A and 2AP effectively blocks transfer from A to 2AP. Base stacking facilitates transfer, while base pairing reduces energy transfer slightly. The efficiency is differentially temperature dependent in single- and double-stranded oligomers and is highest below 0 degrees C in samples measured. An efficiency transition occurs well below the melting transition of a double-stranded decamer. The transfer efficiency in the duplex decamer d(CTGA[2AP]TTCAG)(2) is moderately dependent on the sample and salt concentration and is solvent dependent. Transfer at physiological temperature over more than a few bases is improbable, except along consecutive A's, indicating that singlet energy transfer is not a major factor in the localization of UV damage in DNA. These results have features in common with recently observed electron transfer from 2AP to G in oligonucleotides.

Fluorescence correlations, single molecule detection and large number screening. Applications in biotechnology

Fluorescence correlation spectroscopy (FCS), when carried out under conditions with low background as obtained in very small volume elements, is a powerful tool for examining molecular interactions as well as their time dependence. Interactions of biological importance which can be analyzed are hybridization between nucleic acid primers and DNA or RNA targets, between peptide ligands and isolated as well as cell-bound receptors, between antigen and antibodies. Since the interaction can be analyzed rapidly in small volumes without the need for separating unbound from bound ligand, an important application of FCS is envisaged in large-scale drug screening. The sensitivity has been advanced to the point that detection of single dye molecules is possible in the submillisecond range. This opens up the possibility for detecting rare events such as the appearance of pathogens in the early phase of infection or mutants exhibiting unusual properties when screening combinatorial libraries.

Photochemistry of DNA and related biomolecules: quantum yields and consequences of photoionization

The reactions of nucleic acids and constituents, which can be induced by laser UV irradiation, are described. Emphasis is placed on the quantum yields of various stable photoproducts of DNA and model compounds upon irradiation at 193, 248, 254 or 266 nm. In particular, those quantum yields and processes are discussed which involve photoionization as the initial step and occur in aqueous solution under well defined conditions, e.g. type of atmosphere. The efficiencies of some photoproducts, with respect to photoionization using irradiation at 193 or 248 nm, are presented. Radical cations of nucleobases are important sources of damage of biological substrates since they can cause lesions other than dimers and adducts, e.g. strand breakage, abasic sites, crosslinks or inactivation of plasmid and chromosomal DNA. While competing photoreactions, such as hydration, dimerization or adduct formation, diminish the selectivity of the photoionization method, a combination with model studies on pyrimidine- and purine-containing constituents of DNA has brought about an enhanced insight into the reaction mechanisms. The knowledge concerning the lethal events in plasmid and cellular DNA has been greatly improved by correlation with the chemical effects obtained by gamma-radiolysis, vacuum-UV (< 190 nm) and low-intensity irradiation at 254 nm.

Thermodynamics of interaction of a fluorescent DNA oligomer with the anti-tumour drug netropsin

Fluorescence spectroscopy was used to study the interaction between the minor-groove-binding drug netropsin and the self-complementary oligonucleotide d(CTGAnPTTCAG)2 containing the fluorescent base analogue 2-aminopurine (nP). The binding of netropsin to this oligonucleotide causes strong quenching of the 2-aminopurine fluorescence, observed by steady-state as well as time-resolved spectroscopy. From fluorescence titrations, binding isotherms were recorded and evaluated. The parameters showed one netropsin binding site/oligonucleotide duplex and an association constant of about 10(5) M-1 at 25 degrees C, 3-4 orders of magnitude weaker than for an exclusive adenine/thymine host sequence. From the temperature dependence of the association constant the thermodynamic parameters were obtained as delta G = -29 kJ/mol, delta H = -12 kJ/mol and delta S = +55 J.mol-1.K-1 at 25 degrees C. These parameters resemble those of the interaction of poly[(dG-dC).(dG-dC)] with netropsin, indicating a mainly entropy-driven reaction. The amino group of 2-aminopurine, like that of guanine, resides in the minor groove of DNA. Therefore the relatively weak binding of netropsin to d(CTGAnPTTCAG)2 is probably related to partial blockage of the tight fit of netropsin into the preferred minor groove of an exclusive adenine/thymine host sequence.

Singlet-singlet energy transfer along the helix of a double-stranded nucleic acid at room temperature

An irreversible electronic energy trap has been formed in calf thymus DNA by methylating about 75% of its G bases at position N-7. This has allowed us to measure for the first time the efficiency of transfer of energy along the helix of a double-stranded nucleic acid at room temperature. It is found that about one out of every three photons absorbed by the other bases is trapped. We have also simulated the data with a stochastic model that uses the dipole-dipole interaction to calculate the efficiency of transfer. In order to approximate the experimental results, the model requires that: (i) the fluorescence quantum yield of T, C, and G in DNA be about 2 x 10(-3), which is about two orders of magnitude larger than the value of the fluorescence quantum yield reported for DNA; and (ii) the fluorescence quantum yield of A in DNA be negligibly small. Requirement (i) is consistent with energy transfer taking place before a very efficient fluorescence quenching process sets in, which could be formation of excited-state complexes (excimers) that do not fluoresce appreciably. Requirement (ii) implies a very short fluorescence lifetime for A, which is consistent with the reported absence of a significant number of photoproducts formed by A in DNA. The simulations find that, on the average, the excitation energy takes about 1.2 steps to reach the trap; that is to say, bases that are nearest and next nearest neighbors of the trap are, in effect, the only energy donors. Both intra- as well as interstrand energy transfer (the latter only for the C-trap base pair) make significant contributions. The value of the efficiency for pairwise base-base intrastrand transfer is about 60%, whereas those for base-trap intra- and interstand transfer are 90% and 80%, respectively. The corresponding values for the rate constant of transfer are 2 x 10(11), 1 x 10(12), and 4 x 10(11) s-1. Transfer is inefficient when A is the donor or the acceptor. In addition to the dipole-dipole term, the only other significant term in the expansion of the interaction potential is the dipole-quadrupole term which, however, makes only a small contribution to the overall transfer efficiency. The electron exchange interaction appears to be much less efficient than the coulombic interaction.

Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base

Time-resolved fluorescence decay of a single-stranded DNA decamer d(CTGAAT5CAG), where d5 is the fluorescent base 1-(beta-D-2'-deoxyribosyl)-5-methyl-2-pyrimidinone, was measured and analyzed at several temperatures. The d5 base in the decamer is resolved into three states according to their fluorescence decay lifetime characteristics and temperature dependence of their associated amplitudes: fully extended and completely unstacked state, loosely associated state, and fully stacked state. These states are in slow exchange compared to their fluorescence decay rates. The population of the fully extended and completely unstacked state is small and decreases further with increasing temperature. The loosely associated state, whose fluorescence can still be efficiently quenched by other DNA bases, occupies a large portion of the conventionally defined unstacked state. Stacking enthalpy and entropy for the d5 base with thymine or cytosine bases in the DNA decamer are calculated to be -6.6 kcal/mol and -22 cal/mol.K, respectively. This work shows that fluorescent bases in DNA can be useful to the study of local conformations of bases.

Fluorometric analysis of the long-wavelength absorption band of N-7 methylated GMP into the constituent bands of the two electronic states

Steady-state measurements of fluorescence anisotropy are used to resolve the long-wavelength absorption spectrum of 7-methyl guanosine 5'-monophosphate (GMP) in pH 5 buffer at room temperature into component spectra that correspond to the electronic transitions I and II present in that spectral region. We have chosen this derivative of guanine because its fluorescence quantum yield is much greater than that of GMP. It is found that the data are adequately described by a model that involves emission exclusively from state I, with state II converting to it with 100% efficiency. The shape of the absorption spectrum of state II is virtually independent of the angle theta between the absorption transition dipole moments of states I and II, whereas that of state I is dependent on theta. We analyze the data on the basis of the premise that in the short-wavelength region state II is the predominantly absorbing state. This premise is based on studies of single-crystal polarized reflection and linear dichroism from stretched films. The spectral maxima for the two states are found to be at about 290 and 260 nm, respectively. There is also a weak band which is centered at about 245 nm. The oscillator strengths are found to be 0.07, 0.21 and approximately 0.04, for states I, II and that associated with the weak band, respectively. The importance of these findings with regard to the photophysical properties of nucleic acids and calculations of their CD spectra is discussed.

Two-quantum UV photochemistry of nucleic acids: comparison with conventional low-intensity UV photochemistry and radiation chemistry

The action of high-intensity laser u.v. radiation on nucleic acid molecules and their constituents in vitro and in vivo is compared with the results of low-intensity u.v. photolysis and gamma-radiolysis.

Diffuse reflectance pulse radiolysis of solid DNA: the effect of hydration

Using diffuse reflectance pulse radiolysis, it has been demonstrated from spectral characteristics of the resulting transients that the chemical events following irradiation of DNA depend upon its state of hydration.

Stochastic model of free radical yields in oriented DNA exposed to densely ionizing radiation at 77K

Monte Carlo simulation techniques were used to calculate the probability that thymine radical anions (T.-), formed by the slowing-down of high-energy protons in oriented DNA, will undergo a secondary protonation reaction. By assuming a large asymmetry in the thermal conductivity of oriented DNA fibres we predict a significant enhancement of protonation of T.- when the proton flux is incident on the sample parallel to the orientation of the DNA. These results are in qualitative agreement with experimental data on the production of TH. radicals when oriented DNA is exposed to fast neutrons.