|
|
NUCLEOTIDE BASE PAIRING STRUCTURAL DIAGRAM
|
|
Enlarge image.
|
|
|
|
IUPAC NUCLEOTIDE AMBIGUITY CODES |
| Y = |
T or C (pyrimidine) |
| R = |
G or A (purine) |
| M = |
A or C (amino) |
| K = |
G or T (keto) |
| S = |
G or C (strong interaction; 3 H bonds) |
| W = |
A or T (weak interaction; 2 H bonds) |
| B = |
G or T or C (not A) |
| V = |
G or C or A (not T, not U) |
| D = |
G or A or T (not C) |
| H = |
A or C or T (not G) |
| N = |
G or A or T or C (unknown nucleotide) |
|
|
|
|
COPY NUMBER OF COMMONLY USED PLASMIDS |
| Plasmid |
Plasmid Size (bp)
(approx.) |
Origin of
Replication* |
Copy
Number |
Yield per ml of Culture
(µg)** |
References |
| pGEM® series |
2,700 |
mutated pMB1 |
300-700 |
1.8-4.1 |
1 |
| pUC |
2,700 |
mutated pMB1 |
500-700 |
2.9-4.1 |
1 |
| pBR322 |
4,400 |
pMB1 |
>25 |
>0.23 |
2 |
| ColE1 |
4,500 |
ColE1 |
>15 |
>0.15 |
3 |
| pACYC |
4,000 |
p15A |
~10 |
~0.09 |
4 |
| pSC101 |
9,000 |
pSC101 |
~6 |
~0.12 |
5 |
| HaloTag® pHT2 |
5,000 |
mutated pMB1 |
300-700 |
3.3-7.6 |
1 |
| pGL series |
5,000 |
mutated pMB1 |
300-700 |
3.3-7.6 |
1 |
| pRL series |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| phRL series |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| phRG series |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| pCBG and pCBR series |
5,000 |
mutated pMB1 |
300-700 |
3.3-7.6 |
1 |
| phMGFP |
4,700 |
mutated pMB1 |
300-700 |
3.1-7.1 |
1 |
| pGEM®-T/T Easy |
3,000 |
mutated pMB1 |
300-700 |
2.0-4.6 |
1 |
| pGeneClip™ series |
5,000 |
mutated pMB1 |
300-700 |
3.3-7.6 |
1 |
| psiLentGene™ series |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| psiCHECK™ -1/2 |
4,000-6,000 |
mutated pMB1 |
300-700 |
2.7-9.1 |
1 |
| psiSTRIKE™ series |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| pTNT™ |
2,900 |
mutated pMB1 |
300-700 |
1.9-4.4 |
1 |
| pCMVTNT™ |
4,000 |
mutated pMB1 |
300-700 |
2.7-6.0 |
1 |
| pACT and pBIND series |
6,000 |
mutated pMB1 |
300-700 |
4.0-9.1 |
1 |
pALTER®-1/
EX1 |
5,800 |
pMB1 |
>25 |
>0.3 |
3 |
| pALTER®-EX2 |
5,800 |
p15A |
~10 |
~0.13 |
4 |
| pSP |
2,500 |
mutated pMB1 |
300-700 |
1.6-3.8 |
1 |
| pCI, pSI |
3,600 |
mutated pMB1 |
300-700 |
2.4-5.5 |
1 |
*Plasmids carrying the pMB1, mutated pMB1 and
ColE1 belong to the same incompatibility group and so are not
compatible with one another, but are fully compatible with those
carrying p15A and pSC101 replicons.
**Theoretical plasmid yields were calculated
from the reported copy number and size of each plasmid assuming
2.0 x 106 cells per milliliter of culture grown for 16 hours at
37°C.References
- Summerton, J., Atkins, T. and Bestwick, R. (1983) Anal.
Biochem. 133, 79.
- Holmes, D.S. and Quigley, M. (1981) Anal. Biochem. 114,
193.
- Jansz, H.S., Pouwels, P.H. and Schiphorst, J. (1966) Biochem.
Biophys. Acta 123, 626.
- Birnboim, H.C. and Doly, J. (1979) Nucl. Acids Res. 7,
1513.
- Birnboim, H.C. (1983) Meth. Enzymol. 100, 243.
|
|
|
|
|
PHYSICAL CONSTANTS OF NTPs |
| Compounds |
MW* |
λmax at pH 7.0
(nm) |
Absorbance
at λmax
for 1M Solution
(E; pH
7.0) |
| α-S dATP |
507.3 |
259 |
15,400 |
| α-S dCTP |
483.3 |
271 |
9,100 |
| α-S dGTP |
523.3 |
252 |
13,700 |
| α-S dTTP |
498.3 |
267 |
9,650 |
| ATP |
507.2 |
259 |
15,400 |
| CTP |
483.2 |
271 |
9,000 |
| dITP |
492.2 |
249 |
12,200 |
| dUTP |
468.2 |
262 |
10,200 |
| GTP |
523.2 |
253 |
13,700 |
| UTP |
484.2 |
260 |
10,000 |
| dATP |
491.2 |
259 |
15,400 |
| dCTP |
467.2 |
272 |
9,100 |
| dGTP |
507.2 |
253 |
13,700 |
| dTTP |
482.2 |
267 |
9,600 |
| iso-dC |
481.2 |
260 |
6,300 |
| iso-dG |
507.2 |
292 |
11,000 |
| *Molecular weight of free acid with no waters of
hydration. |
|
|
|
|
CONVERSION FORMULA |
|
(observed absorbance at λmax) = molar conc.
of nucleic acid
absorbance at λmax for 1M solution
Reference
Sambrook, J. and Russell, D.W. (2001) In: Molecular Cloning: A
Laboratory Manual, 3rd ed., Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY. |
|
|
|
LENGTHS AND MOLECULAR WEIGHTS OF COMMON NUCLEIC ACIDS |
| Nucleic Acid |
Number of
Nucleotides |
Molecular
Weight* |
| lambda DNA |
48,502 (dsDNA) |
3.2 x 107 |
| pBR322 DNA |
4,361 (dsDNA) |
2.8 x 106 |
| 28S rRNA |
4,800 |
1.6 x 106 |
| 23S rRNA (E. coli) |
2,900 |
1.0 x 106 |
| 18S rRNA |
1,900 |
6.5 x 105 |
| 16S rRNA (E. coli) |
1,500 |
5.1 x 105 |
| 5S rRNA (E. coli) |
120 |
4.1 x 104 |
| tRNA (E. coli) |
75 |
2.5 x 104 |
| *Molecular weights based on actual sequence. |
|
Standards
- Average MW of a dsDNA base pair = 660.
- Average MW of a ssDNA base = 330.
- Average MW of a RNA base = 340.
References
- Daniels, D.L. et al. (1983) Appendix II: Complete annotated
lambda sequence. In: Lambda II, ed., R.W. Hendrix et al.,
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 519.
- Sutcliffe, J.G. (1978) Proc. Natl. Acad. Sci. USA 75,
3737.
- Sutcliffe, J.G. (1979) Cold Spring Harb. Symp. Quant. Biol.
43, 77.
|
|
|
|
|
|
|
|
-top of page-
|
|
