Vorlesung Biophysik I - Molekulare Biophysik Kalbitzer/Kremer/Ziegler

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1 Vorlesung Biophysik I - Molekulare Biophysik Kalbitzer/Kremer/Ziegler Zelle Biologische Makromoleküle I Biologische Makromoleküle II Nukleinsäuren-Origami (DNA, RNA) Aminosäuren-Origami (Protein-Nanotechnologie) Molekulare Motoren Methoden zur Strukturbestimmung: Magnetische Resonanzspektroskopie I - Grundlagen Magnetische Resonanzspektroskopie II - Mehrdimensionale NMR- Spektroskopie Magnetische Resonanzspektroskopie III Proteinstrukturbestimmung, Dynamik und Bewegung, ESR-Spektroskopie Röntgenstrukturanalyse I Streuung von Wellen, Faltungstheorem, Pattersonfunktion, Phasenproblem Röntgenstrukturanalyse II - Synchrotronstrahlung, zeitaufgelöste Kristallographie Röntgenkleinwinkelstreuung Elektronenmikroskopie I Elektronenoptik, Kontrastentstehung und Bildinformation Elektronenmikroskopie II Kristalline Objekte, Tomographie Klausur

2 DNA-Struktur

3 DNA-Struktur

4 RNA-Struktur

5 RNA-Struktur

6 DNA als Molekül für Nanotechnologen N.C. Seeman, Karriere für die Doppelhelix, Spektrum der Wissenschaften Januar 2005

7 DNA als Molekül für Nanotechnologen 5 -ACCGGGTTTT-3 binds most strongly to 3 -TGGCCCAAAA-5 Less strongly to a sequence with a Hamming distance of 1 from the perfect complement 3 -TGGCCCAAAC-5 Binding strength even less strongly to a sequence of Hamming distance 2, such as 3 -TGGCACAAAC-5, etc. Ordering of binding strength approximately governed by Hamming distance

8 DNA-Kreuzungspunkte mit klebrigen Enden

9 Kreuzungspunkte von DNA

10 DNA Crosslinks

11 DNA-Strukturen

12 DNA Arrays

13 DNA-Würfel

14 Molekularer Schalter auf DNA-Basis

15 DNA-Oktaeder

16 DNA-Origami

17 DNA-Origami

18 DNA- Origami Design

19 DNA- Origami

20 DNA-Origami

21 DNA-Origami (Beispiele)

22 DNA-Origami (Beispiele)

23 DNA-Origami (Beispiele)

24 DNA-Origami (Faltungsbeispiel)

25 DNA-Origami (Faltungsbeispiel)

26 DNA-Origami (Faltungsbeispiel)

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31 DNA-Origami Science 2006

32 DNA-Origami Science 2006

33 DNA-Origami Science 2006

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41 Molecular Logic Gate Components DNA enzymes The switch part for a molecular logic gate is derived from a deoxyribozyme, a nucleic acid enzyme that catalyzes DNA reactions. In this case the enzyme is a phosphodiesterase, which cleaves an oligonucleotide substrate (a short sequence of single-stranded DNA) into two shorter oligonucleotide products, or outputs. M.N. Stojanovic, T.E. Mitchell, & D.Stefanovic (2002) Deoxyribozyme-Based Logic Gates J.Am.Chem.Soc.124,

42 DNA outputs and fluorescence monitoring In order to monitor output formation, the outputs can be labeled with fluorescent dyes. In the case above, the Substrate is labeled with red channel TAMRA (T) dye, but its fluorescence is quenched by the Black-Hole 2 (BH2) quencher, which absorbs all of the TAMRA fluorescence. After cleavage, the TAMRA is separated from the BH2 and the fluorescence is no longer absorbed, leading to an increase in fluorescence within the mixture, which can be monitored via fluorescence spectroscopy. We have successfully used several combinations of fluorescent dye/quencher combinations, including Fluorescein/Black Hole Quencher 1 and Fluorescein/Tamra. The fluorescence is merely a byproduct of the reaction for monitoring purposes. Output formation can be coupled to many different downstream events, such as the activation of a downstream gate, and release of a small molecule such as a drug.

43 DNA inputs and stem-loop controllers The DNA enzyme is turned into a switch that is regulated by input DNA through the addition of specific stem-loop regions, which contain oligonucleotide binding regions. If input DNA (a short single-stranded oligonucleotide) is added, it will hybridize to the oligonucleotide binding region, causing the stem-loop to undergo a conformational change and break apart.. DNA inputs are highly selective, and will only hybridize to their specific complementary sequence. Thus it is possible to have many inputs and stemloop regions in the same mixture without undesirable gate activation from input cross-reactivity. The use of stem-loop controlling structures also makes the gates fully modular, such that many oligonucleotide sequences can be placed for input binding in the loop regions.

44 Types of Molecular Logic gates The YES gate.

45 Types of Molecular Logic gates The NOT gate.

46 Types of Molecular Logic gates The AND gate.

47 Types of Molecular Logic gates The ANDNOT gate.

48 Types of Molecular Logic gates

49 DNA- Elektronik Science 2006

50 DNA- Elektronik Science 2006

51 DNA-Elektronik Science 2006

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57 RNA- Nanotechnologie Purdue scientists treat cancer with RNA nanotechnology Image: This triangular particle, which is about 25 billionths of a meter across, could become one of nanotechnology's contributions to the fight against cancer. Three strands of RNA a close chemical cousin of DNA are linked together to form this "nanoparticle," created in the lab of Purdue University's Peixuan Guo. Each of the strands is spliced together from two kinds of RNA one sort serves as a scaffold and dovetail to hold the particle together; while the other carries a hunter to find cancer cells, a marker to detect the target, or genetic instructions deadly to a cancer cell. The nanoparticles have already proven effective against cancer growth in living mice as well as lab-grown human nasopharlyngeal carcinoma and breast cancer cells. (Guo Laboratories)

58 Vorlesung Biophysik I - Molekulare Biophysik Kalbitzer/Kremer/Ziegler Zelle Biologische Makromoleküle I Biologische Makromoleküle II Nukleinsäuren-Origami (DNA, RNA) Aminosäuren-Origami (Protein-Nanotechnologie) Molekulare Motoren Methoden zur Strukturbestimmung: Magnetische Resonanzspektroskopie I - Grundlagen Magnetische Resonanzspektroskopie II - Mehrdimensionale NMR- Spektroskopie Magnetische Resonanzspektroskopie III Proteinstrukturbestimmung, Dynamik und Bewegung, ESR-Spektroskopie Röntgenstrukturanalyse I Streuung von Wellen, Faltungstheorem, Pattersonfunktion, Phasenproblem Röntgenstrukturanalyse II - Synchrotronstrahlung, zeitaufgelöste Kristallographie Röntgenkleinwinkelstreuung Elektronenmikroskopie I Elektronenoptik, Kontrastentstehung und Bildinformation Elektronenmikroskopie II Kristalline Objekte, Tomographie Klausur

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