24:
37:
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323:. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. The GU
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process can still occur on certain genes in the absence of U2AF2. This may be because 10% of genes in zebrafish have alternating TG and AC base pairs at the 3' splice site (3'ss) and 5' splice site (5'ss) respectively on each intron, which alters the secondary structure of the RNA. This suggests that
485:
together. A single turn of the helix constitutes about ten nucleotides, and contains a major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major
439:
Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Frequently these elements, or combinations of them, are further classified into additional categories including, for example,
610:, which uses a recursive scoring system to identify paired stems and consequently cannot detect non-nested base pairs with common algorithms. However, limited subclasses of pseudoknots can be predicted using modified dynamic programs. Newer structure prediction techniques such as
528:
structure (also often referred to as an "hairpin"), in which a base-paired helix ends in a short unpaired loop, is extremely common and is a building block for larger structural motifs such as cloverleaf structures, which are four-helix junctions such as those found in
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is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low
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contains a pseudoknot that is critical for its activity. The hepatitis delta virus ribozyme is a well known example of a catalytic RNA with a pseudoknot in its active site. Though DNA can also form pseudoknots, they are generally not present in standard
397:, is simple providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. The cell avoids this problem by allowing its DNA-melting enzymes (
1298:
Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (October 1998). "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs".
533:. Internal loops (a short series of unpaired bases in a longer paired helix) and bulges (regions in which one strand of a helix has "extra" inserted bases with no counterparts in the opposite strand) are also frequent.
356:. Melting is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating,
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Pseudoknots can form a variety of structures with catalytic activity and several important biological processes rely on RNA molecules that form pseudoknots. For example, the RNA component of the human
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in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of general pseudoknots in nucleic acid sequences impossible to
658:, or other cases in which base pairs are not fully nested, as considering these structures becomes computationally very expensive for even small nucleic acid molecules. Other methods, such as
646:
Most methods for nucleic acid secondary structure prediction rely on a nearest neighbor thermodynamic model. A common method to determine the most probable structures given a sequence of
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For many RNA molecules, the secondary structure is highly important to the correct function of the RNA — often more so than the actual sequence. This fact aids in the analysis of
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31:
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Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robert; Huang, Yen-Tsung; Fairbrother, William G. (13 November 2015).
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in nucleic acid molecules which is intimately connected with the molecule's secondary structure. A double helix is formed by regions of many consecutive base pairs.
27:
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secondary structure of RNA can influence splicing, potentially without the use of proteins like U2AF2 that have been thought to be required for splicing to occur.
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double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form
28:
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Doudna, Jennifer A.; Ferré-D'Amaré, Adrian R.; Zhou, Kaihong (October 1998). "Crystal structure of a hepatitis delta virus ribozyme".
295:. Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.
641:
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319:; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of singly ringed chemical structures called
1346:"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure"
304:, but contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly and stabilization is mainly due to
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between the two halves of another stem. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true
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can be used to categorize and compare complex structures that arise from combining these elements in various arrangements.
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polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The
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There are many secondary structure elements of functional importance to biological RNAs; some famous examples are the
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This article is about secondary structure in nucleic acid. For the article about secondary structure in protein, see
544:. Active research is on-going to determine the secondary structure of RNA molecules, with approaches including both
405:, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other.
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Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots".
759:. The database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties.
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The secondary structure of nucleic acid molecules can often be uniquely decomposed into stems and loops. The
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algorithm that seeks to find structures with low free energy. Dynamic programming algorithms often forbid
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groove. Many double-helical forms are possible; for DNA the three biologically relevant forms are
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RNA secondary structure can be determined from atomic coordinates (tertiary structure) obtained by
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are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing,
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at the start of many genes to assist RNA polymerase in melting the DNA for transcription.
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The nucleic acid double helix is a spiral polymer, usually right-handed, containing two
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in certain species. In humans and other tetrapods, it has been shown that without the
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rich regions. Particular base steps are also susceptible to DNA melting, particularly
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base steps. These mechanical features are reflected by the use of sequences such as
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Lai, Michael M. C. (1995-06-01). "The
Molecular Biology of Hepatitis Delta Virus".
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Zuker, M. (1989-04-07). "On finding all suboptimal foldings of an RNA molecule".
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unwind the strands to facilitate the advance of sequence-reading enzymes such as
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In a non-biological context, secondary structure is a vital consideration in the
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1505:"DSSR: an integrated software tool for dissecting the spatial structure of RNA"
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Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (May 2004).
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Yakovchuk, Peter; Protozanova, Ekaterina; Frank-Kamenetskii, Maxim D. (2006).
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have canonical long stem-loop structures interrupted by small internal loops.
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A pseudoknot is a nucleic acid secondary structure containing at least two
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Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004).
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1035:"Functional analysis of the pseudoknot structure in human telomerase RNA"
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can also be used to predict nucleic acid secondary structure.
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tend to be different: biological DNA mostly exists as fully
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DNAlive: a web interface to compute DNA physical properties
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883:"Predicting DNA duplex stability from the base sequence"
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protein, the splicing process is inhibited. However, in
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for noncoding but functional forms of RNA. For example,
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uses predicted RNA secondary structures in searching a
327:, with two hydrogen bonds, does occur fairly often in
263:(U). Alternate hydrogen bonding patterns, such as the
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Lu, XJ; Bussemaker, HJ; Olson, WK (2 December 2015).
721:. Current methods include 3DNA/DSSR and MC-annotate.
50:(primary, secondary, tertiary, and quaternary) using
1147:"Pseudoknots: RNA Structures with Diverse Functions"
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200:, a GC base pair demonstrating three intermolecular
1145:Staple, David W.; Butcher, Samuel E. (2005-06-14).
995:Pabo C, Sauer R (1984). "Protein-DNA recognition".
881:Breslauer KJ, Frank R, Blöcker H, Marky LA (1986).
578:structure. For example, the RNA component of human
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275:. Importantly, pairing is the mechanism by which
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783:"Paradigms for computational nucleic acid design"
669:sometimes termed "RNA genes". One application of
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942:"DNA melting temperature - How to calculate it?"
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393:Strand separation by gentle heating, as used in
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590:structures in which half of one stem is
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423:Structural motif § In nucleic acids
40:The image above contains clickable links
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1573:MDDNA: Structural Bioinformatics of DNA
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684:RNA secondary structure applies in
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709:Secondary structure determination
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470:The double helix is an important
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345:Hybridization is the process of
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940:Richard Owczarzy (2008-08-28).
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948:. owczarzy.net. Archived from
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1257:Annual Review of Biochemistry
974:. New York: Garland Science.
970:Alberts; et al. (1994).
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108:interactions within a single
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1033:Chen JL, Greider CW (2005).
401:) to work concurrently with
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1425:10.1126/science.2468181
1371:10.1073/pnas.0401799101
1060:10.1073/pnas.0502259102
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752:Molecular models of DNA
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1509:Nucleic Acids Research
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1039:Proc Natl Acad Sci USA
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640:Further information:
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421:Further information:
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502:Stem-loop structures
255:(C) in DNA. In RNA,
159:Fundamental concepts
114:secondary structures
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1218:1998Natur.395..567F
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608:dynamic programming
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686:RNA splicing
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110:nucleic acid
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763:RNA CoSSMos
656:pseudoknots
648:nucleotides
560:Pseudoknots
446:pseudoknots
321:pyrimidines
313:nucleobases
311:The larger
293:translation
222:nucleotides
126:base paired
106:basepairing
56:VS ribozyme
52:DNA helices
1811:Biophysics
1800:Categories
1760:Proteasome
1719:Prediction
1709:Quaternary
1666:Prediction
1656:Quaternary
1094:J Mol Biol
956:2008-10-02
769:References
696:and other
619:telomerase
580:telomerase
576:pseudoknot
566:Pseudoknot
479:nucleotide
450:stem-loops
442:tetraloops
350:base pairs
302:GC-content
285:anticodons
64:nucleosome
60:telomerase
1699:Secondary
1646:Secondary
1433:0036-8075
1309:CiteSeerX
1277:0066-4154
1173:1545-7885
1151:PLOS Biol
694:zebrafish
679:microRNAs
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526:stem-loop
520:Stem-loop
512:stem-loop
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399:helicases
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698:teleosts
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253:cytosine
247:(T) and
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1745:Protein
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859:1360284
757:DiProDB
604:predict
598:. The
574:An RNA
510:An RNA
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317:purines
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690:U2AF2
496:Z-DNA
492:B-DNA
488:A-DNA
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