254:
553:, is a form of the DNA duplex observed under dehydrating conditions. It is shorter and wider than B-DNA. RNA adopts this double helical form, and RNA-DNA duplexes are mostly A-form, but B-form RNA-DNA duplexes have been observed. In localized single strand dinucleotide contexts, RNA can also adopt the B-form without pairing to DNA. A-DNA has a deep, narrow major groove which does not make it easily accessible to proteins. On the other hand, its wide, shallow minor groove makes it accessible to proteins but with lower information content than the major groove. Its favored conformation is at low water concentrations. A-DNAs base pairs are tilted relative to the helix axis, and are displaced from the axis. The sugar pucker occurs at the C3'-endo and in RNA 2'-OH inhibits C2'-endo conformation. Long considered little more than a laboratory artifice,
564:
favored conformation occurs when there are high salt concentrations. There are some base substitutions but they require an alternating purine-pyrimidine sequence. The N2-amino of G H-bonds to 5' PO, which explains the slow exchange of protons and the need for the G purine. Z-DNA base pairs are nearly perpendicular to the helix axis. Z-DNA does not contain single base-pairs but rather a GpC repeat with P-P distances varying for GpC and CpG. On the GpC stack there is good base overlap, whereas on the CpG stack there is less overlap. Z-DNA's zigzag backbone is due to the C sugar conformation compensating for G glycosidic bond conformation. The conformation of G is syn, C2'-endo; for C it is anti, C3'-endo.
374:
22:
233:, hence the glycosidic bonds form between their 1 nitrogen and the 1' -OH of the deoxyribose. For both the purine and pyrimidine bases, the phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar. The polarity in DNA and RNA is derived from the oxygen and nitrogen atoms in the backbone. Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms. A
579:, which is the tertiary structure of DNA. Supercoiling is characterized by the linking number, twist and writhe. The linking number (Lk) for circular DNA is defined as the number of times one strand would have to pass through the other strand to completely separate the two strands. The linking number for circular DNA can only be changed by breaking of a covalent bond in one of the two strands. Always an integer, the linking number of a cccDNA is the sum of two components: twists (Tw) and writhes (Wr).
475:
33:
483:
456:. It is minimally composed of two helical segments connected by single-stranded regions or loops. H-type fold pseudoknots are best characterized. In H-type fold, nucleotides in the hairpin-loop pair with the bases outside the hairpin stem forming second stem and loop. This causes formation of pseudoknots with two stems and two loops. Pseudoknots are functional elements in RNA structure having diverse function and found in most classes of RNA.
681:
130:
357:. Although the two strands are aligned by hydrogen bonds in base pairs, the stronger forces holding the two strands together are stacking interactions between the bases. These stacking interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a large amount of local structural variability. There are also two grooves in the double helix, which are called
653:. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of nucleic acids. Moreover, it refers to interactions of the nucleic acids with other molecules. The most commonly seen form of higher-level organization of nucleic acids is seen in the form of
377:
An example of RNA secondary structure. This image includes several structural elements, including; single-stranded and double-stranded areas, bulges, internal loops and hairpin loops. Double-stranded RNA forms an A-type helical structure, unlike the common B-type conformation taken by double-stranded
459:
Secondary structure of RNA can be predicted by experimental data on the secondary structure elements, helices, loops, and bulges. DotKnot-PW method is used for comparative pseudoknots prediction. The main points in the DotKnot-PW method is scoring the similarities found in stems, secondary elements
626:
Twists are the number of times the two strands of DNA are twisted around each other. Writhes are number of times the DNA helix crosses over itself. DNA in cells is negatively supercoiled and has the tendency to unwind. Hence the separation of strands is easier in negatively supercoiled DNA than in
567:
A linear DNA molecule having free ends can rotate, to adjust to changes of various dynamic processes in the cell, by changing how many times the two chains of its double helix twist around each other. Some DNA molecules are circular and are topologically constrained. More recently circular RNA was
546:
is the most common form of DNA in vivo and is a more narrow, elongated helix than A-DNA. Its wide major groove makes it more accessible to proteins. On the other hand, it has a narrow minor groove. B-DNA's favored conformations occur at high water concentrations; the hydration of the minor groove
563:
is a relatively rare left-handed double-helix. Given the proper sequence and superhelical tension, it can be formed in vivo but its function is unclear. It has a more narrow, more elongated helix than A or B. Z-DNA's major groove is not really a groove, and it has a narrow minor groove. The most
494:
constraints. It is a higher order than the secondary structure, in which large-scale folding in a linear polymer occurs and the entire chain is folded into a specific 3-dimensional shape. There are 4 areas in which the structural forms of DNA can differ.
253:
237:
is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series of letters. Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. Sequences can be
940:
Katsuyuki, Aoki; Kazutaka, Murayama; Hu, Ning-Hai (2016). "Solid State
Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance". In Astrid, Sigel; Helmut, Sigel; Roland K.O., Sigel (eds.).
547:
appears to favor B-DNA. B-DNA base pairs are nearly perpendicular to the helix axis. The sugar pucker which determines the shape of the a-helix, whether the helix will exist in the A-form or in the B-form, occurs at the C2'-endo.
382:
The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules.
411:
The antiparallel strands form a helical shape. Bulges and internal loops are formed by separation of the double helical tract on either one strand (bulge) or on both strands (internal loops) by unpaired nucleotides.
345:. It has a single ring structure, a six-membered ring containing nitrogen. A purine base always pairs with a pyrimidine base (guanine (G) pairs with cytosine (C) and adenine (A) pairs with thymine (T) or
242:
to another sequence in that the base on each position is complementary as well as in the reverse order. An example of a complementary sequence to AGCT is TCGA. DNA is double-stranded containing both a
309:
Secondary structure is the set of interactions between bases, i.e., which parts of strands are bound to each other. In DNA double helix, the two strands of DNA are held together by
290:
There are three potential metal binding groups on nucleic acids: phosphate, sugar, and base moieties. Solid-state structure of complexes with alkali metal ions have been reviewed.
422:
is formed when the RNA chains fold back on themselves to form a double helical tract called the 'stem', the unpaired nucleotides forms single stranded region called the 'loop'. A
575:
A covalently closed, circular DNA (also known as cccDNA) is topologically constrained as the number of times the chains coiled around one other cannot change. This cccDNA can be
28:
26:
27:
621:
115:. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.
25:
321:
with the nucleotide on the other strand. The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as
1462:
1052:
Hollyfield JG, Besharse JC, Rayborn ME (December 1976). "The effect of light on the quantity of phagosomes in the pigment epithelium".
1089:"The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA"
337:. Purines consist of a double ring structure, a six-membered and a five-membered ring containing nitrogen. The pyrimidines are
490:
Tertiary structure refers to the locations of the atoms in three-dimensional space, taking into consideration geometrical and
958:
873:
848:
800:
261:
such as this four-arm junction. These four strands associate into this structure because it maximizes the number of correct
1560:
1455:
735:
1284:
Chen X; Ramakrishnan B; Sundaralingam M (1995). "Crystal structures of B-form DNA-RNA chimers complexed with distamycin".
982:
Sedova A, Banavali NK (2017). "Geometric
Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands".
720:
239:
1387:
1565:
1555:
1507:
741:
644:
635:. The plectonemic supercoil is found in prokaryotes, while the solenoidal supercoiling is mostly seen in eukaryotes.
1545:
299:
258:
1241:
Dickerson RE, Drew HR, Conner BN, Wing RM, Fratini AV, Kopka ML (April 1982). "The anatomy of A-, B-, and Z-DNA".
1550:
1448:
469:
1512:
1502:
650:
426:
is a four-base pairs hairpin RNA structure. There are three common families of tetraloop in ribosomal RNA:
1327:
Sedova A, Banavali NK (2016). "RNA approaches the B-form in stacked single strand dinucleotide contexts".
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1492:
747:
816:
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453:
373:
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described as well to be a natural pervasive class of nucleic acids, expressed in many organisms (see
243:
47:
1409:
229:
between their 9 nitrogen and the 1' -OH group of the deoxyribose. Cytosine, thymine, and uracil are
1423:
783:
Krieger M, Scott MP, Matsudaira PT, Lodish HF, Darnell JE, Lawrence Z, Kaiser C, Berk A (2004).
1522:
1471:
695:
100:
661:. Also, the quaternary structure refers to the interactions between separate RNA units in the
585:
1540:
234:
124:
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8:
1601:
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257:
Nucleic acid design can be used to create nucleic acid complexes with complicated
145:. It is this linear sequence of nucleotides that make up the primary structure of
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strand. Therefore, the complementary sequence will be to the sense strand.
104:
1305:
1270:
1122:
1087:
Rietveld K, Van
Poelgeest R, Pleij CW, Van Boom JH, Bosch L (March 1982).
1073:
532:
structures have been demonstrated in repetitive polypurine:polypyrimidine
474:
1440:
666:
203:
51:
1297:
1606:
945:. Metal Ions in Life Sciences. Vol. 16. Springer. pp. 43–66.
632:
449:
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or hairpin loop is the most common element of RNA secondary structure.
326:
314:
230:
157:
138:
59:
55:
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353:
of the two polynucleotide strands wrapped around each other to form a
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Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Wlater P (2002).
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839:
Anthony-Cahill SJ, Mathews CK, van Holde KE, Appling DR (2012).
649:
The quaternary structure of nucleic acids is similar to that of
32:
491:
386:
The four basic elements in the secondary structure of RNA are:
349:(U)). DNA's secondary structure is predominantly determined by
346:
322:
222:
207:
187:
1189:"Predicting pseudoknotted structures across two RNA sequences"
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550:
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782:
16:
Biomolecular structure of nucleic acids such as DNA and RNA
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1616:
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191:
181:
150:
146:
112:
108:
1424:"Structural Biochemistry/Nucleic Acid/DNA/DNA structure"
1017:
Tinoco I, Bustamante C (October 1999). "How RNA folds".
657:
which leads to its interactions with the small proteins
1240:
863:
627:
relaxed DNA. The two components of supercoiled DNA are
555:
A-DNA is now known to have several biological functions
1186:
843:(4th ed.). Englewood Cliffs, N.J: Prentice Hall.
508:
Difference in size between the major and minor grooves
834:
832:
830:
588:
46:(primary, secondary, tertiary, and quaternary) using
1138:"Pseudoknots: RNA structures with diverse functions"
676:
1187:Sperschneider J, Datta A, Wise MJ (December 2012).
939:
285:
137:Primary structure consists of a linear sequence of
827:
788:
615:
452:is an RNA secondary structure first identified in
446:is a purine). UNCG is the most stable tetraloop.
1236:
1234:
1232:
1644:
1370:Mirkin SM (2001). "DNA Topology: Fundamentals".
1016:
891:"The emergence of complexity: lessons from DNA"
24:
1326:
1229:
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857:
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221:The nitrogen bases adenine and guanine are
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943:The Alkali Metal Ions: Their Role for Life
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1112:
916:
906:
809:
785:"Section 4.1: Structure of Nucleic Acids"
481:
473:
372:
252:
128:
36:The image above contains clickable links
20:
866:Molecular Biology of the Cell (4th ed.)
638:
153:. Nucleotides consist of 3 components:
1645:
1369:
293:
1444:
463:
882:
736:Nucleic acid structure determination
118:
1136:Staple DW, Butcher SE (June 2005).
888:
721:Non-helical models of DNA structure
442:is one of the four nucleotides and
13:
512:The tertiary arrangement of DNA's
31:
14:
1669:
795:. New York: W.H. Freeman and CO.
742:Nucleic acid structure prediction
645:Nucleic acid quaternary structure
868:. New York NY: Garland Science.
679:
300:Nucleic acid secondary structure
286:Complexes with alkali metal ions
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1320:
1277:
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1080:
470:Nucleic acid tertiary structure
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1010:
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365:based on their relative size.
1:
1205:10.1093/bioinformatics/bts575
769:
505:Number of base pairs per turn
1155:10.1371/journal.pbio.0030213
1066:10.1016/0014-4835(76)90221-9
1019:Journal of Molecular Biology
908:10.1371/journal.pbio.0020431
817:"Structure of Nucleic Acids"
651:protein quaternary structure
141:that are linked together by
7:
996:10.1021/acs.biochem.6b01101
951:10.1007/978-3-319-21756-7_3
748:Nucleic acid thermodynamics
672:
10:
1674:
642:
499:Handedness – right or left
467:
454:turnip yellow mosaic virus
297:
122:
1632:Nucleic acid double helix
1584:
1531:
1478:
1286:Nature Structural Biology
1054:Experimental Eye Research
731:Nucleic acid double helix
133:Chemical structure of DNA
616:{\displaystyle Lk=Tw+Wr}
502:Length of the helix turn
460:and H-type pseudoknots.
225:in structure and form a
1380:10.1038/npg.els.0001038
1263:10.1126/science.7071593
889:Mao C (December 2004).
478:DNA structure and bases
281:. Image from Mao, 2004.
1472:Biomolecular structure
1093:Nucleic Acids Research
1031:10.1006/jmbi.1999.3001
791:Molecular cell biology
696:Biomolecular structure
617:
487:
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379:
368:
304:
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97:Nucleic acid structure
93:
50:and examples from the
44:nucleic acid structure
37:
1105:10.1093/nar/10.6.1929
618:
485:
477:
376:
256:
235:nucleic acid sequence
132:
125:Nucleic acid sequence
35:
30:
639:Quaternary structure
586:
259:secondary structures
1602:Protein engineering
1298:10.1038/nsb0995-733
1255:1982Sci...216..475D
763:Triple-stranded DNA
726:Nucleic acid design
701:Crosslinking of DNA
530:Triple-stranded DNA
486:A-B-Z-DNA Side View
294:Secondary structure
206:(found in DNA) and
143:phosphodiester bond
706:DNA nanotechnology
613:
516:in space includes
488:
480:
464:Tertiary structure
380:
329:. The purines are
283:
135:
94:
38:
1640:
1639:
1341:10.1002/bip.22750
990:(10): 1426–1443.
960:978-3-319-21755-0
875:978-0-8153-3218-3
850:978-0-13-800464-4
802:978-0-7167-4366-8
753:Protein structure
119:Primary structure
40:Interactive image
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1627:Structural motif
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1249:(4545): 475–85.
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202:which is called
158:Nitrogenous base
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1199:(23): 3058–65.
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210:(found in RNA).
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1406:|journal=
1389:978-0470016176
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1292:(9): 733–735.
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1193:Bioinformatics
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311:hydrogen bonds
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298:Main article:
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246:strand and an
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200:5-carbon sugar
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1060:(6): 623–35.
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1025:(2): 271–81.
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835:
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831:
822:
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812:
804:
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786:
779:
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764:
761:
759:
758:Satellite DNA
756:
754:
751:
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746:
743:
740:
737:
734:
732:
729:
727:
724:
722:
719:
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711:DNA supercoil
709:
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688:
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677:
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538:Satellite DNA
535:
531:
527:
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515:
507:
504:
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484:
476:
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268:
264:
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126:
116:
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110:
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105:nucleic acids
102:
98:
90:
86:
82:
78:
74:
70:
66:
61:
57:
53:
49:
45:
41:
19:
1612:Nucleic acid
1533:Nucleic acid
1532:
1427:. Retrieved
1418:
1371:
1365:
1335:(2): 65–82.
1332:
1328:
1322:
1289:
1285:
1279:
1246:
1242:
1196:
1192:
1182:
1145:
1142:PLOS Biology
1141:
1131:
1096:
1092:
1082:
1057:
1053:
1047:
1022:
1018:
1012:
987:
984:Biochemistry
983:
977:
942:
935:
901:(12): e431.
898:
895:PLOS Biology
894:
884:
865:
859:
841:Biochemistry
840:
820:
811:
790:
778:
648:
625:
574:
566:
559:
549:
542:
514:double helix
511:
489:
458:
448:
443:
439:
435:
431:
427:
414:
410:
405:
400:
395:
390:
385:
381:
363:minor groove
359:major groove
355:double helix
351:base-pairing
308:
289:
220:
213:One or more
190:(present in
180:(present in
136:
96:
95:
43:
39:
18:
1429:11 December
1329:Biopolymers
1148:(6): e213.
667:spliceosome
633:plectonemic
577:supercoiled
327:pyrimidines
315:nucleotides
277:matched to
269:matched to
231:pyrimidines
204:deoxyribose
139:nucleotides
52:VS ribozyme
48:DNA helices
1647:Categories
1607:Proteasome
1566:Prediction
1556:Quaternary
1513:Prediction
1503:Quaternary
821:SparkNotes
770:References
450:Pseudoknot
319:base pairs
263:base pairs
60:nucleosome
56:telomerase
1546:Secondary
1493:Secondary
1408:ignored (
1398:cite book
655:chromatin
424:tetraloop
420:Stem-loop
416:Stem-loop
406:Junctions
248:antisense
101:structure
1585:See also
1551:Tertiary
1498:Tertiary
1357:35949700
1349:26443416
1223:23044552
1174:15941360
1039:10550208
1004:28187685
969:26860299
927:15597116
673:See also
663:ribosome
659:histones
629:solenoid
339:cytosine
173:Cytosine
107:such as
1592:Protein
1541:Primary
1488:Primary
1480:Protein
1314:6886088
1306:7552741
1271:7071593
1251:Bibcode
1243:Science
1214:3516145
1165:1149493
1123:7079175
1074:1087245
570:CircRNA
391:Helices
343:thymine
335:guanine
331:adenine
323:purines
265:, with
178:Thymine
168:Guanine
163:Adenine
1571:Design
1518:Design
1386:
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524:, and
492:steric
434:, and
396:Bulges
347:uracil
313:. The
223:purine
208:ribose
188:Uracil
1353:S2CID
1310:S2CID
561:Z-DNA
551:A-DNA
544:B-DNA
526:Z-DNA
522:A-DNA
518:B-DNA
401:Loops
244:sense
194:only)
184:only)
1431:2012
1410:help
1384:ISBN
1345:PMID
1302:PMID
1267:PMID
1219:PMID
1170:PMID
1119:PMID
1070:PMID
1035:PMID
1000:PMID
965:PMID
955:ISBN
923:PMID
870:ISBN
845:ISBN
797:ISBN
631:and
436:CUUG
432:GNRA
428:UNCG
361:and
341:and
333:and
325:and
273:and
111:and
89:1EQZ
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81:4R4V
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73:1BNA
69:ADNA
58:and
54:and
1658:RNA
1653:DNA
1622:RNA
1617:DNA
1376:doi
1372:eLS
1337:doi
1333:105
1294:doi
1259:doi
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1160:PMC
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