Nucleic acids are biological molecules essential for life, and include DNA deoxyribonucleic acid and RNA ribonucleic acid . Together with protein s, nucleic acids make up the most important macromolecule s each is found in abundance in all living things. Nucleic acids were first discovered by Friedrich ... DNA Friedrich Miescher and the early years of nucleic acid research volume 122 issue 6 pages 565 81 issn 0340 6717 doi 10.1007 s00439 007 0433 0 journal Human genetics ref Experimental studies of nucleic ... ref The term nucleic acid is the over all name for DNA and RNA, members of a family of biopolymer s, ref cite journal author Elson D title Metabolism of nucleic acids macromolecular DNA and RNA ... url ref and is synonymous with Polynucleotide polynucleotide . Nucleic acids ... eukaryotic cells, nucleic acids are now known to be found in all life forms, including within ... 2009 pages isbn 0 321 53615 0 oclc doi accessdate ref The basic component of biological nucleic ... group, and a nucleobase . Nucleic acids are also generated within the laboratory, through the use of enzymes ... enable the generation of altered nucleic acids that are not found in nature, ref cite journal author ... url ref for example peptide nucleic acid s. Molecular composition and size ref name Stryer Nucleic ... the largest individual molecules known. Well studied biological nucleic acid molecules range in size ... circumstances, nucleic acid structures with Triple stranded DNA three or G quadruplex four strands can form. Nucleic acids are linear polymer s chains of nucleotides. Each nucleotide consists of three ... a nucleoside . Nucleic acid types differ in the structure of the sugar in their nucleotides DNA ... group . Also, the nucleobases found in the two nucleic acid types are different adenine , cytosine .... The sugars and phosphates in nucleic acids are connected to each other in an alternating chain ... year 2007 pages isbn 0 7167 6766 X oclc doi accessdate ref In nucleic acid nomenclature conventional ... more details
Orphan date February 2009 Nucleic acid metabolism is the process by which nucleotides are synthesized and degraded. Nucleic acid synthesis is an anabolism anabolic mechanism generally involving chemical reaction of phosphate , pentose sugar , and a nitrogenous base . Destruction of nucleic acid is a catabolism catabolic procedure generally involving enzyme reactions. DNA and RNA are the main nucleic acids References Mohamed, M. Optometry Professor. Smith, K. Optometrist. Sohn, S. Biomedical Science Professor of U of W. biochem stub Category Nucleic acids ... more details
Nucleic acid structure refers to the Biomolecular structure structure of nucleic acid s such as DNA and RNA It is often divided into four different levels Nucleic acid primary structure Primary structure &mdash the raw sequence of nucleobase s of each of the component DNA strands Nucleic acid secondary structure Secondary structure &mdash the set of interactions between bases, i.e., which parts of which strands are bound to each other Nucleic acid tertiary structure Tertiary structure &mdash the locations of the atoms in three dimensional space, taking into consideration geometrical and steric constraints and Nucleic acid quaternary structure Quaternary structure &mdash the higher level organization of DNA in chromatin, or to the interactions between separate RNA units in the ribosome or spliceosome . See also Nucleic acid double helix Nucleic acid structure determination experimental Nucleic acid structure prediction computational DNA nanotechnology Nucleic acid design Nucleic acid thermodynamics DNA supercoil molecular biology stub Biomolecular structure Category DNA Category RNA ca Estructura de l ADN es Estructura del cido nucleico tr DNA n n yap s zh DNA ... more details
Threose nucleic acid TNA is a polymer similar to DNA or RNA but differing in the composition of its backbone . TNA is not known to occur naturally. DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas TNA s backbone is composed of repeating threose units linked by phosphodiester bond s. The threose molecule is easier to assemble than ribose making it a possible precursor to RNA. DNA TNA hybrid chains have been made in the laboratory using DNA polymerase. TNA can specifically base pair with RNA and DNA this capability and chemical simplicity suggests that TNA could have preceded RNA as genetic material. See also Abiogenesis Glycol nucleic acid Peptide nucleic acid External links http www.newscientist.com article mg17924052.500.html Was simple TNA the first nucleic acid on Earth to carry a genetic code? , New Scientist http www.sciencemag.org cgi content summary 290 5495 1306 ORIGIN OF LIFE A Simpler Nucleic Acid , Leslie Orgel References cite journal title A Simpler Nucleic Acid last Orgel first Leslie journal Science journal Science year 2000 month November pages 1306 1307 volume 290 issue 5495 doi 10.1126 science.290.5495.1306 pmid 11185405 cite journal title Modified nucleic acids on display last Watt first Gregory journal Nature Chemical Biology year 2005 month February url http www.nature.com nchembio journal vaop nprelaunch full nchembio005.html doi 10.1038 nchembio005 cite journal title Chemical etiology of nucleic acid structure the alpha threofuranosyl 3 2 oligonucleotide system. last Schoning first K coauthors Scholz P Guntha S Wu X Krishnamurthy R Eschenmoser A journal Science journal Science year 2000 month November pmid 11082060 doi 10.1126 science.290.5495.1347 volume 290 pages 1347 51 issue 5495 Nucleic acids Category Nucleic acids Category Polymers genetics stub ca cid treonucleic fr Acide nucl ique thr ose it Acido treonucleico pl TNA ru zh ... more details
infobox journal title Nucleosides, Nucleotides & Nucleic Acids abbreviation Nucleosides Nucleotides Nucleic Acids frequency Monthly country England editor John A. Secrist III publisher Taylor & Francis Informa Healthcare language English ISSN 1525 7770 eISSN 1532 2335 LCCN sn 99004347 website http www.informaworld.com openurl?genre journal&issn 1525 7770 link1 http www.is3na.org link1 name International Society on Nucleosides, Nucleotides and Nucleic Acids link2 http www.ppsociety.org link2 name The Purine and Pyrimidine Society history 2000 present discipline Biochemistry OCLC 41669733 impact 0.768 impact year 2009 Nucleosides, Nucleotides & Nucleic Acids is a monthly academic journal published by Taylor & Francis since 2000, continuing the earlier Nucleosides and Nucleotides in series. It discusses topics relating to the biochemisty of molecules in these classes. med journal stub Category Biochemistry journals Category Publications established in 2000 Category English language publications ... more details
Infobox journal title Nucleic Acids Research cover File Cover Nucleic Acids Research v33i12 small.gif Image Cover Nucleic Acids Research v33i12 small.gif editor Barry L. Stoddard , Keith R. Fox discipline Nucleic acid s peer reviewed language abbreviation Nucleic Acids Res. publisher Oxford University Press country frequency Biweekly history 1974 present openaccess Partial license impact 7.479 impact year 2009 website http nar.oxfordjournals.org link1 http nar.oxfordjournals.org content current link1 name Online access link2 http nar.oxfordjournals.org archive link2 name Online archive JSTOR OCLC 01791693 LCCN 74641038 CODEN NARHAD ISSN 0305 1048 eISSN 1362 4962 Nucleic Acids Research is a peer review peer reviewed scientific journal published by Oxford University Press . It covers research on nucleic acid s, such as DNA and RNA , and related work. Some of its content is available under an Open access publishing open access license. According to the Journal Citation Reports , the journal s 2009 impact factor is 7.479, ranking it 27th out of 283 journals in the category Biochemistry & Molecular Biology . The journal publishes two yearly special issues, one dedicated to biological database s, published in January since 1993 and the other on biological web server s, published in July since 2003. External links Official http nar.oxfordjournals.org Category Biochemistry journals Category Hybrid open access journals Category Publications established in 1974 Category Oxford University Press academic journals Category Biweekly journals Category English language journals biology journal stub fr Nucleic Acids Research ... more details
for protein methods Protein methods Nucleic acid methods are the techniques used to study nucleic acid s DNA and RNA . Purification Guanidinium thiocyanate phenol chloroform extraction Phenol chloroform extraction minicolumn purification Quantification Abundance in weight Quantification of nucleic acids spectroscopic quantification Absolute abundance in number Real time polymerase chain reaction Q PCR high throughput relative abundance DNA microarray high throughput absolute abundance serial analysis of gene expression SAGE Size Gel electrophoresis Synthesis De novo Oligonucleotide synthesis Amplification Polymerase chain reaction PCR Other List of nucleic acid simulation software Nucleic acid simulations DNA sequencing Bisulfite sequencing Expression cloning Southern blot northern blot Sucrose gradient centrifugation Radioactivity in biological research Lab on a chip Nuclear run on Nuclear run on assay Fluorescent in situ hybridization several Bioinformatics methods, such as List of RNA structure prediction software RNA structure prediction See also CSH Protocols External links http www.genome.ou.edu protocol book protocol index.html PROTOCOLS FOR RECOMBINANT DNA ISOLATION, CLONING, and SEQUENCING Molecular Biology Category Molecular biology ca M todes dels cids nucleics zh ... more details
Image Mao 4armjunction schematic.png thumb 250px Nucleic acid design can be used to create nucleic acid complexes with complicated Nucleic acid secondary structure secondary structures such as this four ... pages 2036 2038 issn 1544 9173 doi 10.1371 journal.pbio.0020431 pmc 535573 pmid 15597116 ref Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing . ref name Dirks04 It is necessary because there are many possible Nucleic acid sequence sequences of nucleic acid strands that will fold into a given Nucleic acid secondary structure secondary ... be avoided. In addition, there are many Nucleic acid tertiary structure tertiary structure considerations ... name Sherman06 Nucleic acid design has similar goals to protein design in both, the sequence of monomers .... However, nucleic acid design has the advantage of being a much computationally simpler problem ... structure tertiary structure information whereas nucleic acid design can operate largely on the level of Nucleic acid secondary structure secondary structure . However, nucleic acid structures are less versatile than proteins in their functionality. ref name Dirks04 ref name Brenneman02 Nucleic acid design can be considered the inverse of nucleic acid structure prediction . In structure prediction, the structure is determined from a known sequence, while in nucleic acid design, a sequence is generated ... structure.svg thumb 250px Chemical structure of DNA. Nucleic acid double helices will only form ... bases are matched into only A T or G C pairs. The Nucleic acid structure structure of nucleic acids ... T . Nucleic acids have the property that two molecules will bind to each other to form a double ... form matching sequences of base pair s. Thus, in nucleic acids the sequence determines the pattern ... Theoretical Computer Science volume 287 pages 39 ref Nucleic acid design is the process by which ... more details
Unreferenced date December 2009 Image Numbered cytidine.png thumb Numbered ribose carbons on cytidine . Molecular biologist s use several shorthand terms when referring to nucleic acid molecules, such as DNA and RNA , collectively referred to as nucleic acid nomenclature . The most common is the representation of the base pair s as letters&mdash an adenine nucleotide is abbreviated as A , guanine as G , cytosine as C , thymine as T , and in RNA, uracil as U . Additionally, the positions of the carbon s in the ribose sugar that forms the backbone of the nucleic acid chain are numbered, and are used to indicate the direction of nucleic acids 5 3 versus 3 5 , see directionality molecular biology directionality . Expanded letter code In addition to the conventional GATC symbols, there is an expanded letter code to indicate a position within a sequence that may be flexible when defining sequences. class wikitable border 1 Letter Nucleotide s included A A T T G G C C R G or A Y T or C M A or C K G or T S G or C W A or T H A or C or T B G or T or C V G or C or A D G or T or A N G or T or A or C For example, if the sequences known to bind protein X are known to be AAAAAAGAAA, AAAAAACAAA, AAAAAATAAA, and AAAAAAAAAA, this can be expressed as AAAAAANAAA. Triple Helix Base Pairing Watson and Crick base pairs are indicated by a or a or a . Example A T, or poly rC 2poly rC Hoogsteen base pairs are indicated by a or a Example C G G , or T A T, or C G G, or T A A See also DNA replication Nucleotide BranchesofChemistry Natural sciences footer DEFAULTSORT Nucleic Acid Nomenclature Category DNA replication Category Nucleic acids Category Nucleotides Interlanguage links de Nukleins ure Nomenklatur ... more details
In molecular biology , analysis of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acid s often require particular amounts and purity for optimum performance. There are several methods to establish the concentration of a solution of nucleic acids, including spectrophotometric quantification and UV fluorescence in presence of a DNA dye. Spectrophotometric analysis Nucleic acids Absorption electromagnetic radiation absorb ultraviolet light in a specific pattern. In a spectrophotometer ... through the sample. The more light absorbed by the sample, the higher the nucleic acid concentration ... It is common for nucleic acid samples to be contaminated with other molecules i.e. proteins, organic ... the purity of nucleic acids. For pure DNA, A sub 260 280 sub is 1.8 and for pure RNA A sub 260 ... affect the 260 280 ratio in a nucleic acid solution. ref name molecular cloning ref cite journal author Glasel J. year 1995 title Validity of nucleic acid purities monitored by 260nm 280nm absorbance ... high sensitivity for nucleic acid contamination in protein border 1 protein nucleic acid 260 280 ... in nucleic acids border 1 nucleic acid protein 260 280 ratio 100 0 2.00 95 5 1.99 90 10 1.98 70 30 1.94 This difference is due to the much higher extinction coefficient nucleic acids have at 260nm ... is commonly used in nucleic acid purification, can significantly throw off quantification estimates. Phenol absorbs with a peak at 270nm and a A sub 260 280 sub of 2. Nucleic acid preparitions uncontaminated ... range. The value in a pure nucleic acid sample should be zero. Citation needed date January 2010 Negative ... to nucleic acids and selectively fluoresce when bound eg. Ethidium bromide . This method is useful ... also Nucleic acid methods http RNA integrity.gene quantification.info RNA quality control Guanidinium ... Nucleic Acid Purity pdf document http openwetware.org wiki Quantitating nucleic acids double stranded ... more details
Glycol nucleic acid GNA is a polymer similar to DNA or RNA but differing in the composition of its backbone . GNA is not known to occur naturally. The 2,3 dihydroxypropylnucleoside analogues were first prepared by Ueda et al. 1971 . Soon thereafter it was shown that phosphate linked oligomers of the analogues do in fact exhibit hypochromicity in the presence of RNA and DNA in solution Seita et al. 1972 . The preparation of the polymers was later described by Cook et al. 1995, 1999 and Acevedo and Andrews 1996 . The GNA GNA self pairing described by Zhang and Meggers is however novel, and the specificity of interaction well demonstrated. DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas GNA s backbone is composed of repeating glycerol units linked by phosphodiester bond s. The glycerol molecule has just three carbon atoms and still shows Watson Crick base pairing. Interestingly, the Watson Crick base pairing is much more stable in GNA than its natural counterparts DNA and RNA as it requires a high temperature to melt a duplex of GNA. It is possibly the simplest of the nucleic acids, so making it a hypothetical precursor to RNA. See also Abiogenesis Threose nucleic acid Peptide nucleic acid Locked nucleic acid References cite journal author Zhang Lilu, Peritz Adam, Meggers Eric title A simple glycol nucleic acid journal J Am Chem Soc volume 127 issue 12 pages 4174 5 year 2005 url http pubs.acs.org doi pdf 10.1021 ja042564z?cookieSet 1 pmid 15783191 doi 10.1021 ja042564z Seita, Tooru Yamauchi, Kiyoshi Kinoshita, Masayoshi Imoto, Minoru. Condensation polymerization of nucleotide analogues. Die Makromolekulare Chemie 1972 , 154 255 261. Ueda, Nasuo Kawabata, Toshio Takemoto, Kiichi. Synthesis of N 2,3 dihydroxypropyl derivatives of nucleic bases. Journal of Heterocyclic Chemistry 1971 , 8 5 , 827 9. Acevedo, Oscar L. Andrews, Robert S. Synthesis ... 83 i12 8312notw8.html Simpler than DNA Chemical and engineering news Nucleic acids Category Nucleic ... more details
File 220px Molbio Header.svg Small .png thumb Image illustrates DNA, RNA, and protein synthesis. The first two are nucleic acid s. A Nucleic acid inhibitor is a type of antibacterial that acts by inhibiting the production of nucleic acid s. There are two major classes DNA inhibitors and RNA inhibitors. ref http www.ccsf.edu Departments Biology ctoebe antibiotics.htm ref The antifungal flucytosine acts in a similar manner. DNA inhibitors DNA inhibitors such as the quinolones , acting upon DNA gyrase as a topoisomerase inhibitor s ref name SC Another group of DNA inhibitors, including nitrofurantoin and metronidazole , act upon anaerobic bacteria. ref cite pmid 25874 ref These act by generating metabolites that are incorporated into DNA strands, which then are more prone to breakage. ref Cite book last1 P. Denyer first1 Stephen last2 Hodges first2 Norman A. last3 P. Gorman first3 Sean title Hugo and Russell s pharmaceutical microbiology year 2004 publisher Blackwell Science location Oxford isbn 0 632 06467 6 pages 215 ref These drugs are selectively toxic to anaerobic organisms, but can affect human cells. RNA inhibitors RNA inhibitors such as rifampin , acting upon RNA dependent RNA polymerase ref name SC http pathmicro.med.sc.edu mayer antibiot.htm ref Antifolates DNA, RNA, and protein Antifolate s act primarily as inhibitors of both RNA and DNA, and are often grouped with nucleic acid inhibitors in textbooks. However, they also act indirectly as protein synthesis inhibitor s because tetrahydrofolate is also involved in the synthesis of amino acids serine and methionine , so they are sometimes considered as their own category, antimetabolite s. ref http www.life.umd.edu classroom bsci424 Chemotherapy AntibioticMechanisms.htm ref However, the term antimetabolite , when used literally, can apply to many different classes of drugs. References reflist Major drug groups Nucleic acid inhibitors category Antibiotics antibiotic stub sr Inhibitori nukleinskih kiselina ar ... more details
Image PNA en.svg right Peptide Nucleic Acid PNA is an artificially synthesized polymer similar to DNA or RNA invented by Peter E. Nielsen Univ. Copenhagen , Michael Egholm Univ. Copenhagen , Rolf H. Berg Ris National Lab , and Ole Buchardt Univ. Copenhagen in 1991. ref cite journal doi 10.1126 science.1962210 author Nielsen PE, Egholm M, Berg RH, Buchardt O title Sequence selective recognition of DNA by strand displacement with a thymine substituted polyamide journal Science volume 254 issue 5037 pages 1497 500 year 1991 month December pmid 1962210 url http www.sciencemag.org cgi pmidlookup?view long&pmid 1962210 ref DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas PNA s backbone is composed of repeating N 2 aminoethyl glycine units linked by peptide bond s. PNA is not known to occur naturally. The various purine and pyrimidine bases are linked to the backbone by Methylenes methylene carbonyl bonds. PNAs are depicted like peptide s, with the Nitrogen N terminus at the first left position and the Carbon C terminus at the right. ref cite journal doi 10.1038 ... PNA binding is stronger than PNA DNA binding. Synthetic peptide nucleic acid oligomers have been used ... PE, Buchardt Ole, Egholm M, and Nord n B title DNA like Double Helix formed by Peptide Nucleic Acid ... cgi content abstract 97 8 3868 title Peptide nucleic acids rather than RNA may have been ... Glycol nucleic acid Threose nucleic acid References Reflist Further reading cite web author Nielsen ... cite journal author Shabih Shakeel, et al. title Peptide Nucleic Acid PNA A Review journal Journal ... retrieve pii S1074552103002175 cite journal author Ng P S, Bergstrom DE title Alternative Nucleic ... nucleic acids PNAs a new generation of probes for genetic and cytogenetic analyses journal ... A New Game of Life cite journal author Nielsen PE, Egholm M title An Introduction to Peptide Nucleic ... cimb v v1 09.pdf format PDF Nucleic acids DEFAULTSORT Peptide Nucleic Acid Category Nucleic ... more details
on the principles that nucleic acids absorb ultraviolet light in a specific pattern. In the case ... molecule. The following absorbance units to nucleic acid concentration conversion factors are used to convert OD to concentration of unknown nucleic acid samples. A260 dsDNA 50 g ml A260 ssDNA ... ml Most spectrophotometers, like the AQ 07 Nucleic Acid Meter, allow selection of the nucleic acid ... for nucleic acid quantitation is the ability to determine sample purity using the 260 nm 280 ... of protein contamination that is left from the nucleic acid isolation process since proteins absorb at 280 nm. There are many spectrophotometric options available for the quantitation of nucleic ... difference between the NanoDrop is often cost prohibitive for labs needing to quantitate nucleic acids but cannot afford a 9000 spectrophotometer. The AQ 07 Nucleic Acid meter provides a reliable ... 07.php Official AQ 07 Webpage Category Spectroscopy DEFAULTSORT Spectrophotometer For Nucleic Acid ... more details
A nucleic acid test , often called a NAT test, or nucleic acid amplification test NAAT is a biochemistry biochemical technique used to detect a virus or a Bacteria bacterium . These tests were developed to shorten the window period , a time when a patient has been infected and when they show up as positive by ELISA antibody tests . The term includes any test that directly detects the genetic material of the infecting organism or virus. There are multiple methods that fall in this group, including Methods based on the Polymerase chain reaction . These tests use a primer to rapidly make copies of the genetic material. A reverse transcriptase PCR RT PCR is used for HIV and other RNA viruses. Transcription mediated amplification uses a slightly different molecular method than PCR but has the same basic principle. Branched DNA quantiplex bDNA tests use a molecule that links to the specific genetic material. Ligase chain reaction Med diagnostic stub de Nuclein Acid Amplification Test Technology Category Medical diagnosis ... more details
File NATC scheme.png thumb The schematic presentation how the nucleic acid templated chemistry works within cells File NATC reaction.png thumb Schematic presentation of chemical reaction within cells to combine two precursors into an active drug Nucleic acid templated chemistry NATC , or DNA templated chemistry , is principally a new tool to synthesize chemical compounds. The main advantage of the NAT chemistry NATC is performing of the chemical reaction as an intramolecular reaction. The two oligonucleotides or their analogues are linked via chemical groups to precursors of chemical compounds. The oligonucleotides recognize specific nucleic acids and are hybridized sterically close to each other. Afterwards the chemical active groups interact with each other to combine the precursors into a completely new chemical compound. NATC is usually used to perform the synthesis of complex compounds without need to protect chemically active groups during the synthesis. In 1999 Pavel Sergeev suggested to use NATC to synthesize biologically active compounds within living organisms. ref Sergeev, Pavel, Patent application, WO200061775, filling date 08 April 1999 http www.wipo.int pctdb en wo.jsp?wo 2000061775 Synthesis of biologically active compounds in cells PCT IB1999 000616. ref The main idea is to use NATC to synthesize specific biologically active compounds within human cells. The precursors are distributed in the whole human body and the chemical reactions are performed only within ... as to visualize them. ref cite journal author Franzini RM Kool ET title Efficient nucleic acid detection ... chain functionalized peptide nucleic acid aldehydes. journal J Am Chem Soc. volume 130 issue 14 pages ... ref ref cite journal author Miller GP, Silver AP, Kool ET. title New, Stronger Nucleophiles for Nucleic ... N. title DNA templated homo and heterodimerization of peptide nucleic acid encoded oligosaccharides ... L, Merten CA, Winssinger N. title Imaging of mRNA in live cells using nucleic acid templated ... more details
The secondary structure of a nucleic acid molecule refers to the basepair ing interactions within a single ... in a nucleic acid molecule. ref cite journal last Dirks first Robert M. authorlink coauthors Lin, Milo Winfree, Erik & Pierce, Niles A. year 2004 month title Paradigms for computational nucleic acid design journal Nucleic Acids Research volume 32 issue 4 pages 1392 1403 issn doi 10.1093 nar gkh291 ... context, secondary structure is a vital consideration in the Nucleic acid design rational design of nucleic acid structures for DNA nanotechnology and DNA computing , since the pattern of basepairing ... and functional nucleic acid tertiary structure tertiary structures . Importantly, pairing is the mechanism ... of the DNA double helix . Nucleic Acids Research 2006 34 2 564 574 doi 10.1093 nar gkj454 PMID ... often in RNA . Nucleic acid hybridization File DNA orbit animated static thumb.png thumb 150px Two Complementarity molecular biology complementary regions of nucleic acid molcules will bind and from ... right 1.66 C C or G G align right 1.97 A C or G T align right 2.04 G C align right 2.70 Main Nucleic ... the strands of the double helix are broken, separating the two nucleic acid strands. These bonds ... at certain points in the nucleic acid. ref name Breslauer1986 cite journal doi 10.1073 pnas.83.11.3746 ... of sequence reading enzymes such as DNA polymerase . Secondary structure motifs Nucleic acid secondary ... Nucleic acid double helix The double helix is an important Nucleic acid tertiary structure tertiary ... handed spiral polymer of nucleic acids , held together by nucleotides which base pairing base ... of nucleic acid molecules can often be uniquely decomposed into stems and loops. The stem loop structure ... attempting to determine the secondary structure of RNA molecules. Approaches include both Nucleic acid structure determination experimental and Nucleic acid structure prediction computational methods ..., they are generally not present in biological DNA. Secondary structure prediction Main Nucleic ... more details
The nucleic acid notation currently in use was first formalized by the International Union of Pure and Applied Chemistry IUPAC in 1970. ref name iupac1 cite doi 10.1021 bi00822a023 ref This universally accepted notation uses the Roman characters G, C, A, and T, to represent the four nucleotides commonly found in deoxyribonucleic acids DNA . Given the rapidly expanding role for genetic sequencing, synthesis, and analysis in biology, researchers have been compelled to develop alternate notations to further support the analysis and manipulation of genetic data. These notations generally exploit size, shape, symmetry to accomplish these objectives. IUPAC notation class wikitable style margin left 25px margin top 0px float right Symbol ref name iupac Description colspan 4 Bases represented A adenosine A C cytidine C G guanosine G T thymidine T U uridine U W w eak A T S s trong C G M a m ino A C K k eto G T R pu r ine A G Y p y rimidine C T B not A B comes after A C G T D not C D comes after ... Bases in Nucleic Acid Sequences accessdate 2008 02 04 ref representation for a position on a DNA sequence that can be have multiple possible alternatives. These should not be confused with nucleic ... . Under the commonly used IUPAC system, nucleic acids are represented by the first letters of their chemical ... for incompletely specified basis in nucleic acid sequences. Recommendations 1984. Proc. Natl ... shapes to encode lengthy nucleic acid sequences. Several of these approaches are summarized below. Stave ... notations Additional functionality can be found in nucleic acid notations that use ambigrams to mirror ... and pedagogical advantages of an ambigraphic nucleic acid notation. Nucleosides Nucleotides and Nucleic Acids 25 807 813. ref An ambigraphic nucleic acid notation also makes it easy to identify genetic ... data. The latest in a series of rationally designed nucleic acid notations, AmbiScript combines many ... ref As its name implies, AmbiScript is an ambigraphic nucleic acid notation that permits rapid ... more details
nucleotide s, usually representing a single amino acid . The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bond s that those atoms. Because nucleic acids, such as DNA and RNA , are unbranched polymers, this specification ... as a succession of letters representing a real or hypothetical nucleic acid molecule or strand ... used. Sequences can be read from the biological raw material through DNA sequencing methods. Nucleic ... Nucleotide Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists ... make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobase s. The nucleobases are important in base pair ing of strands to form higher level Nucleic acid secondary structure secondary and Nucleic acid tertiary structure tertiary structure such as the famed Nucleic acid double helix double helix . The possible letters are A , C , G , and T , representing ... strand, will have the complementary sequence to the sense strand. Notation Main Nucleic ... Specified Bases in Nucleic Acid Sequences , NC IUB, 1984. ref A adenine C cytosine G guanine T thymine ... after the nucleic acid chain has been formed. In DNA, the most common modified base is 5 methylcytidine ... code , by which the information contained in nucleic acid s are Translation genetics translated ... In biological systems, nucleic acids contain information which is used by a living Cell biology cell to construct specific protein s. The sequence of nucleobase s on a nucleic acid strand is Translation ... using information contained in nucleic acids. DNA is Transcription genetics transcribed into mRNA ... of the protein strand. Since nucleic acids can bind to molecules with Complementarity molecular biology .... Digital representation File AMY1gene.png thumb 370px Genetic sequence in digital format. Once a nucleic ... from 699 vertebrate messenger RNAs journal Nucleic Acids Res. volume 15 issue 20 pages 8125 8148 ... more details
Distinguish degenerate bases For phosphoramidite synthesis of nucleic acids Oligonucleotide synthesis ... and DNA to the right. Nucleic acid analogues are compounds structurally similar Analog chemistry analog to naturally occurring RNA and DNA , used in medicine and in molecular biology research. Nucleic ... self complementary peptide nucleic acid PNA oligomer showing a duplex triplex network. J Am Chem Soc. 2005 Feb 9 127 5 1424 30. ref Artificial nucleic acids include peptide nucleic acid PNA , Morpholino and locked nucleic acid LNA , as well as GNA nucleic acid glycol nucleic acid GNA and TNA nucleic acid threose nucleic acid TNA . Each of these is distinguished from naturally occurring DNA or RNA ... analogues Nucleic acid analogues are used in molecular biology for several purposes As a tool to detect ... scenarios of the origin of life Investigation of the structural features of nucleic acids Investigation ... common RNA analogues are locked nucleic acid Locked nucleic acid LNA , morpholino , and peptide nucleic acid Peptide nucleic acid PNA . These oligonucleotides differ as they have a different backbone ... hypothesis RNA may be too complex to be the first nucleic acid, so before the RNA world hypothesis RNA world several simpler nucleic acids that differ in the backbone, such as TNA nucleic acid TNA and GNA nucleic acid GNA and Peptide nucleic acid PNA , have been offered as candidates for the first nucleic acids. Base analogues Nucleobase structure and nomenclature main Nucleobase Natural bases are divided ... reduced appr. 100 times but highly dependent on base sequence when incorporated into nucleic acids. ref ... nucleic acid containing a substituted phenylpyrrolo cytosine designed to engage guanine with an additional ... base analogs as probes of nucleic acid structure, dynamics and interactions. Curr. Org. Chem. 2002 ... systems. Org, & Biomol. Chem. 2006 4 4265 74. ref ref Wilhelmsson Fluorescent nucleic acid base ... into DNA negligible influence of neighbouring bases on fluorescence quantum yield. Nucleic ... more details
Nucleic acid thermodynamics is the study of the thermodynamics of nucleic acid molecules, or how temperature affects nucleic acid structure . For multiple copies of DNA molecules, the melting temperature T sub m sub is defined as the temperature at which half of the DNA strands are in the Nucleic acid ... covalent , sequence specific interaction between two or more complementary strands of nucleic acid ... to as melting. Here, the solution of hybrids is heated to break the hydrogen bond s between nucleic ... for polymerase chain reaction . Most commonly, the pairs of nucleic bases A T and G C are formed ... gradient gel electrophoresis journal Nucleic Acids Research year 1987 volume 15 pmid 3601667 issue ... Denaturation biochemistry Nucleic acid denaturation renaturation of complementary strands that were ... 1990 title Optimization of the annealing temperature for DNA amplification in vitro. journal Nucleic ... cgi bin abstract 40314 ABSTRACT pdf ref One problem in nucleic acid thermodynamics is to determine the thermodynamic parameters for forming double stranded nucleic acid AB from single stranded nucleic acids A and B. AB A B The equilibrium constant for this reaction is math K frac A B .... This gives, for the nucleic acid system, math Delta G circ RT ln frac A B AB math . The melting temperature, T sub m sub , occurs when half of the double stranded nucleic acid has dissociated. If no additional nucleic acids are present, then A , B , and AB will be equal, and equal to half the initial concentration of double stranded nucleic acid, AB sub initial sub . This gives an expression for the melting point of a nucleic acid duplex of math T m frac Delta G circ R ln frac AB ... stranded state and the random coil state. However, nucleic acids may melt several intermediate ... a nucleic acid duplex is math Delta G 37 circ total Delta G 37 circ initiation sum i 1 10 n i Delta ... eight of the ten groups are independent. A more realistic way of modeling the behavior of nucleic ... more details
About the computational prediction of nucleic acid structure experimental methods Nucleic acid structure determination Nucleic acid structure prediction is a computational method to determine Nucleic acid structure nucleic acid secondary and tertiary structure from its sequence. Secondary structure can be predicted from a single or from several nucleic acid sequences. Tertiary structure can be predicted ... . The problem of predicting nucleic acid secondary structure is dependent mainly on base pair ing ... to a known class of nucleic acid molecules, such as transfer RNA or microRNA , is observed. Many ... for hydrogen bond ing in the nucleic acid backbone. The Nucleic acid thermodynamics energy parameters are also different for the two nucleic acids. Single sequence structure prediction A common ... given just the nucleic acid sequence. However, in the case of RNA much of the final structure ... Non coding RNA List of RNA structure prediction software List of nucleic acid simulation software ... consensus structure from nucleic acid sequences. Comput. Appl. Biosci, . 7, 347 352 ref ref name ... sampling algorithm for RNA secondary structure prediction url journal Nucleic Acids Res. volume 31 ... grammars url http nar.oxfordjournals.org cgi content abstract 31 13 3423 journal Nucleic Acids Res ... based models. J Comput Biol 7 3 4 409 427. ref ref name Macke98 Macke T, Case D Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. Edited by Leontes N, SantaLucia JJ. Washington .... 2004 ILM a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Research .... Nucleic Acids Research, 32 Web Server issue , W142 145. ref ref name Touzet07 Touzet, H., 2007. Comparative ... sequences using thermodynamics and auxiliary information. Nucleic Acids Res. Jan 10 9 1 133 48. ref ... cite journal doi 10.1093 nar gkg595 author Zuker M year 2003 title Mfold web server for nucleic acid folding and hybridization prediction url journal Nucleic Acids Research volume 31 issue 13 pages 3406 ... more details
about the experimental determination of nucleic acid structure computational methods Nucleic acid structure prediction Structure probing of nucleic acid s is the process by which biochemical techniques are used to determine nucleic acid structure . ref cite book author Teunissen AWM title RNA Structure Probing Biochemical structure analysis of autoimmune related RNA molecules year 1979 pages 1 27 isbn 9090132341 ref This analysis can be used to define the patterns which can infer the molecular structure, experimental analysis of molecular structure and function, and further understanding on development of smaller molecules for further biological research. ref cite book author Pace NR, Thomas BC, Woese CR title Probing RNA Structure, Function, and History by Comparative Analysis year 1999 pages 113 117 publisher Cold Spring Harbor Laboratory Press isbn 0879695897 ref Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, SHAPE, nucleotide analog interference mapping NAIM , and in line probing. RNA sequencing While methods for each type of probing differ in steps, the probing of secondary structure involves certain ... sulfate , known as DMS, is a chemical that can be used to modify nucleic acids in order to determine ... hydroxyl radicals which then can react with the nucleic acid molecules. ref name hydrox cite ... used in conjunction with chemical probing of nucleic acid molecules that are thought to associate with proteins ... nucleic acids by the proteins thought to be associated or folding on itself, where cleavage ... than the full nucleic acid depending upon where it is cleaved. In this case since the last ..., or if no protein associates with the nucleic acid it can be caused by the tertiary fold. ref name ... title Ligand recognition determinants of guanine riboswitches journal Nucleic Acids Research volume ... ref name naimm References Reflist Biomolecular structure DEFAULTSORT Nucleic Acid Structure Determination ... more details
structures. Double helix main Nucleic acid double helix The double helix is the dominant tertiary ... url http www.nature.com nature dna50 watsoncrick.pdf title A Structure for Deoxyribose Nucleic Acid ... nucleic acid structures journal J. Mol. Biol. volume 301 issue 3 pages 575 84 year 2000 month ... 10.1038 26912 url issn ref An effect similar to coaxial stacking has been observed in Nucleic acid ... Williams DH, Gait MJ, Loakes D authorlink editor others title Nucleic Acids in Chemistry and Biology .... In the early stages, RNA forms Nucleic acid secondary structure secondary structure s stabilized ... solvent study including conformational adaptation journal Nucleic Acids Res. volume 29 issue ... is vital in stabilizing these kinds of junctions in Nucleic acid design artificially designed structures ... cite journal author Watson JD, Crick FH title Molecular structure of nucleic acids a structure for deoxyribose nucleic acid. J.D. Watson and F.H.C. Crick. Published in Nature, number 4356 April ... be overcome largely because of two major advancements in nucleic acid research the identification ... 1990s has caused a veritable explosion in the field of nucleic acid structural research. Since the publication ... structure Category RNA ca Estructura terci ria de l acid nucleic ... more details
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