The interaction of light within tissue has been used to recognize disease since the mid-1800s. The recent developments of small light sources, detectors, and fiber optic probes provide opportunities to quantitatively measure these interactions, which yield information for diagnosis at the biochemical, structural, or (patho)physiological level within intact tissues. However, because of the strong scattering properties of tissues, the reemitted optical signal is often influenced by changes in biochemistry (as detected by these spectroscopic approaches) and by physiological and pathophysiological changes in tissue scattering. One challenge of biomedical optics is to uncouple the signals influenced by biochemistry, which themselves provide specificity for identifying diseased states, from those influenced by tissue scattering, which are typically unspecific to a pathology. In this review, we describe optical interactions pursued for biomedical applications (fluorescence, fluorescence lifetime, phosphorescence, and Raman from cells, cultures, and tissues) and then provide a descriptive framework for light interaction based upon tissue absorption and scattering properties. Finally, we review important endogenous and exogenous biological chromophores and describe current work to employ these signals for detection and diagnosis of disease.

Quantitative optical spectroscopy for tissue diagnosis

Tm is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. Beyond a simple numerical value (the Tm), a thermal denaturation experiment, in which the folded fraction of a structure is plotted vs. temperature, yields important thermodynamic information. We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves.

Analysis of thermal melting curves

Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each me...

Metal Sensing by DNA

RNA folding into stable tertiary structures is remarkably sensitive to the concentrations and types of cations present; an understanding of the physical basis of ion-RNA interactions is therefore a prerequisite for a quantitative accounting of RNA stability. This article summarizes the energetic factors that must be considered when ions interact with two different RNA environments. “Diffuse ions” accumulate near the RNA because of the RNA electrostatic field and remain largely hydrated. A “chelated” ion directly contacts a specific location on the RNA surface and is held in place by electrostatic forces. Energetic costs of ion chelation include displacement of some of the waters of hydration by the RNA surface and repulsion of diffuse ions. Methods are discussed for computing both the free energy of the set of diffuse ions associated with an RNA and the binding free energies of individual chelated ions. Such calculations quantitatively account for the effects of Mg 2+ on RNA stability where

/pdf/a-guide-to-ions-and-rna-structure-4vheaf1zfz.pdf

A guide to ions and RNA structure

Optical spectroscopy has been extensively studied as a potential in vivo diagnostic tool that can provide information about both the chemical and morphologic structure of tissue in near real time. Most in vivo studies have concentrated on elastic scattering and fluorescence spectroscopies since these signals can be obtained with a good signal-to-noise ratio quickly. However, Raman spectroscopy, an inelastic scattering process, provides a wealth of spectrally narrow features that can be related to the specific molecular structure of the sample. Because of these advantages, Raman spectroscopy has been used to study static and dynamic properties of biologically important molecules in solution, in single living cells, in cell cultures, and more recently, in tissues. This article reviews recent developments in the attempt to develop diagnostic techniques for precancers and cancers, based on Raman spectroscopy. The article surveys important transformations that
occur as tissues progress from normal to precancer and cancerous stages. We briefly review the extensive
literature that summarizes the features and interpretation of Raman spectra of these molecules in solution, and in progressively more complex biological systems. Finally, spectra obtained from intact tissues are comprehensively reviewed and discussed in terms of the molecular and microscopic literature to develop a framework for analyzing Raman signals to yield information about the molecular changes that occur with neoplasia. The article concludes with our perspective on the potential role of Raman spectroscopy in diagnosing precancer and cancerous tissues.

https://www.spiedigitallibrary.org/journals/Journal-of-Biomedical-Optics/volume-1/issue-1/0000/Raman-spectroscopy-for-the-detection-of-cancers-and-precancers/10.1117/12.227815.pdf

Raman spectroscopy for the detection of cancers and precancers

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+.

https://www.cell.com/biophysj/pdf/S0006-3495(96)79528-0.pdf

G.J. Thomas

Papers

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+.

DNA melting investigated by differential scanning calorimetry and Raman spectroscopy.