Курсовая работа по биофизике

«Механические свойства одиночной молекулы ДНК »

БМТ1-61

Студент Зуев Арсений Андреевич

Цель работы — способствовать более глубокому усвоению студента­ми лекций, привитию им навыков самостоятельного мышления, сис­тематизации современных данных об особенностях молекулярного строения живых систем, о малых и больших молекулах в живых системах, о молекулах РНК и ДНК их механических свойствах и связи этих свойств с их функциональными особенностями.

Курсовая работа изучению особенностей механических свойств молекул дезоксирибонуклеиновой кислоты. Работа выполняется в 6-ом семестре и за­щищается перед комиссией, состоящей из преподавателей курса, в зачетную сессию.

В курсовой работе выполняются литературный обзор по следующим вопросам:

1. ДНК и ее роль в живых системах

2. Особенности строения ДНК

3. Физико-химические свойства молекул ДНК

4. Особенности механических свойств одиночных молекул ДНК

5. Взаимосвязь механических свойств молекул ДНК с их функциональными особенностями

Требования к оформлению и содержанию расчетно-пояснительной записки.

Пояснительная записка является результатом проделанной работы и должна быть представлена в виде отдельного журнала с листами, объемом 20-40 стр. печатного текста (шрифт 12 пунктов) выполнен­ного на одной стороне листа с полями (слева - 3 см, справа 1 см, сверху и снизу - 1,5 см) и переплетенного по левому краю. Записка должна быть аккуратно оформлена и иметь:

титульный лист, на котором указывается: Ф.И.О. студента, группа, название работы и номера вариантов, Ф.И.О. руково­дителя и дата завершения работы; оглавление; введение; основная часть; заключение; список литературы; приложение: текст отлаженной программы;

Во введении формулируется основная задача исследования.

В литературном обзоре освещается современное со­стояние вопроса.

В основной части приводятся:

1. Современные представления о ДНК и ее роли в живых системах

2. Строение ДНК

3. Физические и химические свойства молекул ДНК

4. Сравнение механических свойств одиночных молекул ДНК со свойствами

других крупных биополимеров

5) Анализ Взаимосвязи механических свойств молекул ДНК с их

функциональными особенностями

6) Выводы.

Основная литература:

1. Волькенштейн М.В. Молекулярная биофизика М. Наука 1975, 616с
2. Спирин А.С. Молекулярная биология: Структура рибосомы и биосинтез белка. М.: Высш.

шк., 1986.
3. Агол В.И. и др. Молекулярная биология. Структура и биосинтез нуклеиновых кислот. Под

ред. А.С.Спирина. М., Высшая школа, 1990г.

Дополнительная литература

1. Альберте Б. и др. Молекулярная биология клетки. М.,Мир, 1994 .

2. Льюин Б. Гены. М., Мир, 1987 г.

3. УотсонД. Молекулярная биология гена. М., Мир, 1978 г.

4. Хесин Р.Б. Непостоянство генома. М., "Наука", 1984 г.

5. Dickerson RE (1989). "Definitions and nomenclature of nucleic acid structure components". Nucleic Acids Res 17 (5): 1797-1803. PMID 2928107. 

6. ^ Lu XJ, Olson WK (1999). "Resolving the discrepancies among nucleic acid conformational analyses". J Mol Biol 285 (4): 1563-1575. PMID 9917397. 

7. ^ Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, Berman HM (2001). "A standard reference frame for the description of nucleic acid base-pair geometry". J Mol Biol 313 (1): 229-237. PMID 11601858. 

8. ^ Richmond, et al (2003). "The structure of DNA in the nucleosome core". Nature 423: 145-150. PMID 12736678. 

9. ^ Vargason JM, Eichman BF, Ho PS (2000). "The extended and eccentric E-DNA structure induced by cytosine methylation or bromination". Nature Structural Biology 7: 758-761. 

10. ^ ^{a b} Allemand, et al (1998). "Stretched and overwound DNA forms a Pauling-like structure with exposed bases". PNAS 24: 14152-14157. PMID 9826669. 

11. ^ List of 55 fiber structures

12. ^ Crick FH (1976). "Linking numbers and nucleosomes". Proc Natl Acad Sci USA 73 (8): 2639-43. PMID 1066673. 

13. ^ Prunell A (1998). "A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues". Biophys J 74 (5): 2531-2544. PMID 9591679. 

14. ^ Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, "Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution", Nature. 1997 Sep 18; 389 (6648): 251-60.

15. ^ Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution.", Journal of Molecular Biology. 2002 Jun 21; 319 (5): 1097-1113.

Mechanical properties of DNA

The mechanical properties of DNA, which are directly related to its structure, are a significant problem for cells. Every process which binds or reads DNA is able to use or modify the mechanical properties of DNA for purposes of recognition, packaging and modification. The extreme length (a chromosome may contain a 10 cm long DNA strand), relative rigidity and helical structure of DNA has led to the evolution of histones and of enzymes such as topoisomerases and helicases to manage a cell's DNA. The properties of DNA are closely related to its molecular structure and sequence, particularly the weakness of the hydrogen bonds and electronic interactions that hold strands of DNA together compared to the strength of the bonds within each strand.

Experimental techniques which can directly measure the mechanical properties of DNA are relatively new, and high-resolution visualization in solution is often difficult. Nevertheless, scientists have uncovered large amount of data on the mechanical properties of this polymer, and the implications of DNA's mechanical properties on cellular processes is a topic of active current research.

It is important to note the DNA found in many cells can be macroscopic in length - a few centimetres long for each human chromosome. Consequently, cells must compact or "package" DNA to carry it within them. In eukaryotes this is carried by spool-like proteins known as histones, around which DNA winds. It is the further compaction of this DNA-protein complex which produces the well known mitotic eukaryotic chromosomes.

Base pair geometry

The geometry of a base pair can be entirely characterised by 6 coordinates: rise, twist, slide, shift, tilt, and roll. These values precisely define the location and orientation in space of each base pair in a DNA molecule relative to its predecessor along the axis of the helix. Together, they characterise the helical structure of the molecule. In regions of a DNA molecule where the normal structure is disrupted these values are used to describe the disruption.

For each base pair, considered relative to its predecessor^[1][2][3]:

Shear 

Buckle 

Stretch 

Propeller twist

Rotation of one base with respect to the other in the same base pair.

Stagger 

Opening 

Shift 

displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.

Tilt 

rotation around this axis.

Slide 

displacement along an axis in the plane of the base pair directed from one strand to the other.

Roll 

rotation around this axis.

Rise 

displacement along the helix axis.

Twist 

rotation around the helix axis.

x-displacement 

y-displacement 

inclination 

tip 

Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small. A diagram of these coordinates can be found in 3DNA website.

Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. This corresponds to slide between a succession of base pairs, and in helix-based coordinates is properly termed "inclination".

[edit] DNA helix geometries

Three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The "B" form described by James D. Watson and Francis Crick is believed to predominate in cells^[4]. It is 23.7 Å wide and extends 34 Å per 10 bp of sequence. The double helix makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain.

Other conformations are possible; A-DNA, B-DNA, C-DNA, D-DNA, E-DNA^[5], L-DNA, P-DNA^[6], S-DNA, and Z-DNA have been described so far.^[7] As mentioned above C-DNA, D-DNA, E-DNA, and P-DNA have not been observed in naturally occurring biological systems. Also note the triple-stranded DNA possibility.

[edit] A- and Z-DNA

A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallographic experiments, and possibly in hybrid pairings of DNA and RNA strands. Segments of DNA that cells have methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis the opposite way to A-DNA and B-DNA. There is also evidence of protein-DNA complexes forming Z-DNA structures.

The structures of A-, B-, and Z-DNA.

The helix axis of A-, B-, and Z-DNA.

Structural features of the three major forms of DNA
Geometry attribute	A-DNA	B-DNA	Z-DNA
Helix sense	right-handed	right-handed	left-handed
Repeating unit	1 bp	1 bp	2 bp
Rotation/bp	33.6°	35.9°	60°/2bp
Mean bp/turn	10.7	10.0	12
Inclination of bp to axis	+19°	-1.2°	-9°
Rise/bp along axis	2.3 Å	3.32 Å	3.8 Å
Pitch/turn of helix	24.6 Å	33.2 Å	45.6 Å
Mean propeller twist	+18°	+16°	0°
Glycosyl angle	anti	anti	C: anti, G: syn
Sugar pucker	C3'-endo	C2'-endo	C: C2'-endo, G: C2'-exo
Diameter	25.5 Å	23.7 Å	18.4 Å

Supercoiled DNA

See also: DNA supercoil and Mechanical properties of DNA#DNA topology

The B form of the DNA helix twists 360° per 10.4-10.5 bp in the absence of torsional strain. But many molecular biological processes can induce torsional strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled". DNA in vivo is typically negatively supercoiled, which facilitates the unwinding (melting) of the double-helix required for RNA transcription.

Non-helical forms

Other non-double helical forms of DNA have been described, for example side-by-side (SBS) and triple helical configurations. Single stranded DNA may exist 'in statu nascendi' or as thermally induced despiralized DNA.

DNA Bending

DNA is a relatively rigid polymer, typically modelled as a worm-like chain. It has three significant degrees of freedom; bending, twisting and compression, each of which cause particular limitations on what is possible with DNA within a cell. Twisting/torsional stiffness is important for the circularisation of DNA and the orientation of DNA bound proteins relative to each other and bending/axial stiffness is important for DNA wrapping and circularisation and protein interactions. Compression/extension is relatively unimportant in the absence of high tension.

Persistence length/Axial stiffness

Main article: Persistence length

Example sequences and their persistence lengths (B DNA)
Sequence	Persistence Length /base pairs
Random	154±10
(CA)repeat	133±10
(CAG)repeat	124±10
(TATA)repeat	137±10

DNA in solution does not take a rigid structure but is continually changing conformation due to thermal vibration and collisions with water molecules, which makes classical measures of rigidity impossible. Hence, the bending stiffness of DNA is measured by the persistence length, defined as: