Search results for "fluoresenssi"

Rasterikuvakorrelaatiospektroskopiamittauksia Nikon A1R+ -konfokaalimikroskoopilla

2014

Rasterikuvakorrelaatiospektroskopia (RICS) on kvantitatiivinen mikroskopiamenetelmä molekyylidynamiikan tutkimiseen kaksiulotteisista konfokaalikuvista. Tutkielmassa käydään läpi menetelmän teoreettiset ja kokeelliset lähtökohdat, ja niiden pohjalta määritetään kaupallisen konfokaalimikroskooppijärjestelmän (Nikon A1R+, Jyväskylän yliopiston Nanotiedekeskus) soveltuvuus diffuusion mittaamiseen RICS-menetelmällä. Järjestelmän havaittiin soveltuvan heikosti erityisesti nopeiden molekyylien, kuten EGFP-proteiinin mittaamiseen. Suurin haitta oli ilmaisimen häiriösignaali, jonka seurauksena korrelaatioanalyysin tulokset poikkesivat merkittävästi kirjallisuusarvoista. Työssä tehtiin lisäksi yleis…

On dynamics of parvoviral replication protein NS1

2010

Dielectrophoretic trapping and Raman spectroscopy of fluorescent oligonucleotides

2016

Nanotiede kasvaa edelleen tutkimusalana nopeasti, ja sille löytyy lukematon määrä sovelluskohteita. Sen vahvuutena on poikkitieteellisyys fysiikan, kemian ja biologian kesken, jotka kaikki tutkivat atomitason ilmiöitä. Näiden ilmiöiden tutkiminen ja soveltaminen vaatii paljon erilaisia, sofistikoituneita menetelmiä ja työkaluja, joilla voidaan valmistaa ja karakterisoida erilaisia nanopartikkeleita ja -rakenteita. Joissain tapauksissa vaaditaan jopa yksittäisten molekyylien tai atomien manipulointia nanometritasolla. DNA on yksi mielenkiintoisista nanotieteen tutkimuskohteista. Se on elämän kannalta merkittävä molekyyli, sillä se pitää sisällään elävän organismin rakenteellisen ohjeen. DNA:…

Serial femtosecond crystallography reveals that photoactivation in a fluorescent protein proceeds via the hula twist mechanism

2023

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crys…

Fluorescence labeling of the photosensory unit of Deinococcus radiodurans bacteriophytochrome for Förster resonance energy transfer studies

2016

Fytokromit ovat bakteerien, levien, kasvien ja sienten punaista valoa aistivia proteiineja. Keskeinen piirre fytokromien toiminnassa on valon vaikutuksesta tapahtuva siirtymä punaista valoa absorboivan (Pr) ja kaukopunaista valoa absorboivan (Pfr) tilan välillä. Deinococcus radiodurans -bakteerifytokromin valosensoriosa (CBD-PHY) on dimeerinen proteiini, joka koostuu C-terminaalisesta kromoforia sitovasta domeenista (CBD) ja fytokromiin liittyvästä domeenista (PHY). Viimeaikaiset CBD-PHY:n kristalli- ja liuosrakenteet ovat osoittaneet, että PHY-domeenien välinen etäisyys kasvaa, kun proteiini siirtyy Pr-tilasta Pfr-tilaan absorboituaan punaista valoa. Tässä työssä suunniteltiin Försterin re…

Revisited Dual Luminescence of 2,2′-Dipyridylamine Hydrochloride in Solution and Physical Processes behind It

2018

Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization

2022

In recent years, the studies of RNA and its use for the development of RNA based vaccines have increased drastically. Although cyanine dyes are commonly used probes for studying nucleic acids, in a wide range of applications, there is still a growing need for better and brighter dyes. To meet this demand, we have systematically studied the structure of SYBR green-related cyanine dyes to gain a deeper understanding of their interactions with biomolecules especially how they interact with nucleic acids and the structural components which makes them strongly fluorescent. Herein, five new dyes were synthesized, and their photophysical properties were evaluated. Observations of photophysical cha…

Covalent and non-covalent coupling of a Au102 nanocluster with a fluorophore : energy transfer, quenching and intracellular pH sensing

2021

Interactions between an atomically precise gold nanocluster Au102(p-MBA)44 (p-MBA = para mercaptobenzoic acid) and a fluorescent organic dye molecule (KU, azadioxatriangulenium) are studied. In solution, the constituents form spontaneously a weakly bound complex leading to quenching of fluorescence of the KU dye via energy transfer. The KU can be separated from the complex by lowering pH, leading to recovery of fluorescence, which forms a basis for an optical reversible pH sensor. However, the sensor is not a stable entity, which could be delivered inside cells. For this purpose, a covalently bound hybrid is synthesized by linking the KU dye to the ligand layer of the cluster via an ester b…

Rapid Quantification of Microalgae Growth with Hyperspectral Camera and Vegetation Indices

2021

Spectral cameras are traditionally used in remote sensing of microalgae, but increasingly also in laboratory-scale applications, to study and monitor algae biomass in cultures. Practical and cost-efficient protocols for collecting and analyzing hyperspectral data are currently needed. The purpose of this study was to test a commercial, easy-to-use hyperspectral camera to monitor the growth of different algae strains in liquid samples. Indices calculated from wavebands from transmission imaging were compared against algae abundance and wet biomass obtained from an electronic cell counter, chlorophyll a concentration, and chlorophyll fluorescence. A ratio of selected wavebands containing near…

Automated water quality monitoring of humic lakes by using the optical properties of water

2016

Automated water quality monitoring (AWQM) is becoming increasingly common in lakes worldwide. The history of AWQM is relatively short and standard calibration procedures for the measured variables are largely yet to be established. The use of optical AWQM sensors, developed in oceanic environments, raises new questions on the diverse effects which humic compounds may have on the automated optical measurements in inlands waters. The focus of this thesis was to characterize the effects of coloured dissolved organic matter (CDOM) on optical in situ measurements of organic matter (OM) and chlorophyll (Chl) in lakes with varying humic content, and to use AWQM data as a part of traditional monito…