Technical info
Fluorescent Dye | Ex λ (nm) | Em λ (nm) |
| Alexa Fluor 405 | 401 | 421 |
| Alexa Fluor 430 | 433 | 541 |
| ATTO 425 | 436 | 484 |
| DABCYL | 452 | 0 |
| ATTO 465 | 453 | 508 |
| Cy2™ | 489 | 506 |
| Fluoresceine | 491 | 515 |
| FAM | 494 | 518 |
| Alexa Fluor 488 | 495 | 519 |
| MAR | 495 | 525 |
| ATTO 495 | 495 | 527 |
| ATTO 488 | 501 | 523 |
| ATTO 488 | 501 | 523 |
| 500 XXL | 505 | 555 |
| ATTO 520 | 516 | 538 |
| Alexa Fluor 514 | 517 | 542 |
| JOE | 520 | 548 |
| TET | 521 | 538 |
| R6G | 524 | 557 |
| Rhodamine | 524 | 557 |
| JUP | 525 | 550 |
| YAKIMA YELLOW | 531 | 549 |
| ATTO 532 | 532 | 553 |
| ATTO 532 | 532 | 553 |
| Alexa Fluor 532 | 532 | 553 |
| HEX | 535 | 553 |
| CAL Fluor Orange 560 | 537 | 558 |
| CY 3 | 546 | 572 |
| QUASAR 570 | 550 | 570 |
| TAMRA | 550 | 575 |
| ATTO 550 | 554 | 576 |
| NED alternative | 554 | 576 |
| Alexa Fluor 555 | 555 | 565 |
| SAT | 555 | 580 |
| Alexa Fluor 546 | 556 | 573 |
| ATTO 565 | 563 | 592 |
| PET alternative | 563 | 592 |
| ROX | 575 | 602 |
| Alexa Fluor 568 | 578 | 603 |
| Cy 3,5 | 581 | 596 |
| TEXAS RED | 587 | 609 |
| CAL Fluor Red 610 | 590 | 610 |
| Alexa Fluor 594 | 590 | 617 |
| ATTO 590 | 594 | 624 |
| ATTO 590 | 594 | 624 |
| ATTO 594 | 601 | 627 |
| ATTO 611X | 611 | 681 |
| Alexa Fluor 610 | 612 | 628 |
| ATTO 610 | 615 | 634 |
| CAL Fluor Red 635 | 616 | 637 |
| ATTO 620 | 619 | 643 |
| ATTO 633 | 629 | 657 |
| Alexa Fluor 633 | 632 | 647 |
| ATTO 635 | 635 | 659 |
| ATTO 637 | 635 | 659 |
| CY 5 | 643 | 667 |
| ATTO 647N | 644 | 669 |
| ATTO 647 | 644 | 669 |
| QUASAR 670 | 644 | 670 |
| ATTO 647 | 645 | 669 |
| Alexa Fluor 647 | 650 | 665 |
| Beckman Dye D4 | 650 | 670 |
| ATTO 655 | 663 | 684 |
| Alexa Fluor 660 | 663 | 690 |
| Cy 5,5 | 678 | 704 |
| Alexa Fluor 680 | 679 | 702 |
| ATTO 680 | 680 | 700 |
| IRD 700 | 685 | 705 |
| ATTO 700 | 700 | 719 |
| Alexa Fluor 700 | 702 | 723 |
| ATTO 725 | 729 | 752 |
| ATTO 740 | 740 | 764 |
| Alexa Fluor 750 | 749 | 775 |
| Beckman Dye D2 | 750 | 770 |
| IRD 800 | 795 | 819 |
Quantitation of DNA samples
The sample is measured at 260 nm and the absorbance value is used in the concentration calculation.
µg/ml = [Abs at 260 nm * Dilution factor] / [ ε oligo * Pathlength]
(extinction coefficient value) is calculated by the Beckman Oligo Quant software and is based on the base composition of the oligonucleotide.
Melting temperature
Biolegio uses two formulas to calculate the melting point temperarture (Tm) of the oligos.
For short oligos (< 30 bases) the nearest neighbour model is used.
Tm = ΔH˚/[ΔS˚ + 1.987 * In (C/4)] - 273.15 + 16.6 * log[Salt Conc.]
For long oligos (> 30 bases) the following equation is used.
Tm = 81.5 ˚C + 16.6 * log [Salt Conc.] -675/N + 0.41 [% GC]
Deterimination of molecular weight (mw) for the oligo
MW = MWA *[nA] + MWC * [nC] + MWG *[nG] + MWT *[nT] + MWN* [nN] +18.02
MWA = 313.20
MWC = 289.20
MWG = 329.20
MWT = 304.20
MWN = 308.95
The standard genetic code
U | C | A | G | ||||||||
| U | UUU | Phe | UCU | Ser | UAU | Tyr | UGU | Cys | U | ||
| UUC | Phe | UCC | Ser | UAC | Tyr | UGC | Cys | C | |||
| UUA | Leu | UCA | Ser | UAA | Stop | UGA | Stop | A | |||
| First Position | UUG | Leu | UCG | Ser | UAG | Stop | UGG | Trp | G | Third Position | |
| C | CUU | Leu | CCU | Pro | CAU | His | CGU | Arg | U | ||
| CUC | Leu | CCC | Pro | CAC | His | CGC | Arg | C | |||
| CUA | Leu | CGA | Pro | CAA | Gln | CGA | Arg | A | |||
| CUG | Leu | CCG | Pro | CAG | Gln | CGG | Arg | G | |||
| A | AUU | Ile | ACU | Thr | AAU | Asn | AGU | Ser | U | ||
| AUC | Ile | ACC | Thr | AAC | Asn | AGC | Ser | C | |||
| AUA | Ile | ACA | Thr | AAA | Lys | AGA | Arg | A | |||
| AUG | Met | ACG | Thr | AAG | Lys | AGG | Arg | G | |||
| First Position | G | GUU | Val | GCU | Ala | GAU | Asp | GGU | Gly | U | Third Position |
| GUC | Val | GCC | Ala | GAC | Asp | GGC | Gly | C | |||
| GUA | Val | GCC | Ala | GAA | Glu | GGA | Gly | A | |||
| GUG | Val | GCG | Ala | GAG | Glu | GGG | Gly | G | |||
Abbreviations for amino acids
| Ala | Alanine | M | Met | Methionine | |
| B | Asx | Asparagine / aspartic acid | N | Asn | Aparagine |
| C | Cys | Cysteine | P | Pro | Proline |
| D | Asp | Aspartic acid | Q | Gln | Glutamine |
| E | Glu | Glutamic acid | R | Arg | Arginine |
| F | Phe | Phenylalanine | S | Ser | Serine |
| G | Gly | Glycine | T | Thr | Threonine |
| H | His | Histidine | V | Val | Valine |
| I | Ile | Isoleucine | W | Trp | Tryptophan |
| K | Lys | Lysine | Y | Tyr | Tyrosine |
| L | Leu | Leusine | Z | Glx | Glutamine / glutamic acid |
IUB codes
For degenerated oligos, please be sure to use the standard codes given below to mark you mixes-base positions.
| G | Guanine | S (Strong) | C or G |
| A | Adenine | W (Weak) | A or T |
| T | Thumine | B (not A) | C or G or T |
| C | Cytosine | D (not C) | G or A or T |
| R (puRine) | A or G | H (not G) | A or C or T |
| Y (pYrimidine) | C or T | V (not T) | A or C or G |
| M (aMino) | A or C | N (aNy) | A or C or G or T |
| K (Keto) | G or T | X | Label |